5JBH

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN conformation

Present annotations:

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Product Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K [auth Y]	SCOP2B Superfamily	Zn-binding ribosomal proteins	8088663	3001320	SCOP2B (2022-06-29)
L [auth H]	SCOP2B Superfamily	Ribosomal protein S7	8065991	3000799	SCOP2B (2022-06-29)
M [auth K]	SCOP2B Superfamily	Ribosomal protein S5 domain 2-like	8082675	3000100	SCOP2B (2022-06-29)
N [auth M]	SCOP2B Superfamily	Translational machinery components	8100262	3000571	SCOP2B (2022-06-29)
P [auth Q]	SCOP2B Superfamily	S15/NS1 RNA-binding domain	8052956	3001284	SCOP2B (2022-06-29)
P [auth Q]	SCOP2B Superfamily	Homeodomain-like	8052955	3000001	SCOP2B (2022-06-29)
R [auth A]	SCOP2B Superfamily	Ribosomal S3Ae-like	8053209	3002166	SCOP2B (2022-06-29)
S [auth B]	SCOP2B Superfamily	SIS domain/Ribosomal protein S2-like	8063808	3001397	SCOP2B (2022-06-29)
T [auth V]	SCOP2B Superfamily	Ribosomal proteins S24e L23 and L15e	8082571	3000210	SCOP2B (2022-06-29)
U [auth W]	SCOP2B Superfamily	Zn-binding ribosomal proteins	8063782	3001320	SCOP2B (2022-06-29)
W [auth E]	SCOP2B Superfamily	Translation proteins SH3-like KOW motif containing domain	8052754	3000334	SCOP2B (2022-06-29)
W [auth E]	SCOP2B Superfamily	Nucleic acid-binding proteins	8052753	3000135	SCOP2B (2022-06-29)
W [auth E]	SCOP2B Superfamily	Alpha-L RNA-binding motif	8052752	3001473	SCOP2B (2022-06-29)
Y [auth G]	SCOP2B Superfamily	GS N-terminal domain-like	8053162	3000408	SCOP2B (2022-06-29)
Z [auth I]	SCOP2B Superfamily	Ribosomal protein S8	8079067	3000709	SCOP2B (2022-06-29)
AA [auth J]	SCOP2B Superfamily	50S Ribosomal protein L14-like	8053085	3000433	SCOP2B (2022-06-29)
C [auth 3]	SCOP2B Superfamily	L30e-like	8063952	3001739	SCOP2B (2022-06-29)
GA [auth 6]	SCOP2B Superfamily	Nucleic acid-binding proteins	8085842	3000135	SCOP2B (2022-06-29)
HA [auth 7]	SCOP2B Superfamily	Ras-like P-loop GTPases	8056814	3002022	SCOP2B (2022-06-29)
HA [auth 7]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056817	3002024	SCOP2B (2022-06-29)
HA [auth 7]	SCOP2B Superfamily	EF-Tu post-G domain-like	8056815	3002024	SCOP2B (2022-06-29)
JA [auth 9]	SCOP2B Superfamily	Nucleic acid-binding proteins	8037024	3000135	SCOP2B (2022-06-29)
JA [auth 9]	SCOP2B Superfamily	eIF-2-alpha C-terminal domain	8036122	3001618	SCOP2B (2022-06-29)
JA [auth 9]	SCOP2B Superfamily	eIF2alpha middle domain-like	8037022	3001761	SCOP2B (2022-06-29)
D [auth L]	SCOP2 Family	Ribosomal protein S10	8098821	4001240	SCOP2 (2022-06-29)
D [auth L]	SCOP2 Superfamily	Ribosomal protein S10	8098822	3001336	SCOP2 (2022-06-29)
E [auth O]	SCOP2 Family	Ribosomal protein S13	8100259	4000260	SCOP2 (2022-06-29)
E [auth O]	SCOP2 Superfamily	S13-like H2TH domain	8100260	3000053	SCOP2 (2022-06-29)
F [auth P]	SCOP2B Superfamily	Glucocorticoid receptor-like (DNA-binding domain)	8052588	3000068	SCOP2B (2022-06-29)
G [auth S]	SCOP2B Superfamily	Rps17e-like	8063510	3001852	SCOP2B (2022-06-29)
I [auth U]	SCOP2B Superfamily	Winged helix DNA-binding domain	8003150	3000034	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J [auth X]	Ribosomal_S28e	e5jbhX1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosomal_S28e	ECOD (1.6)
K [auth Y]	Ribosomal_S27	e5jbhY1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_S27	ECOD (1.6)
L [auth H]	Ribosomal_S7	e5jbhH1	A: alpha arrays	X: Ribosomal protein S7 (From Topology)	H: Ribosomal protein S7 (From Topology)	T: Ribosomal protein S7	F: Ribosomal_S7	ECOD (1.6)
M [auth K]	Ribosomal_S9	e5jbhK1	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Ribosomal_S9	ECOD (1.6)
N [auth M]	Ribosomal_S11	e5jbhM1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: Ribosomal_S11	ECOD (1.6)
O [auth N]	Ribosom_S12_S23	e5jbhN1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosom_S12_S23	ECOD (1.6)
P [auth Q]	Ribosomal_S13_N_1	e5jbhQ2	A: alpha arrays	X: HTH	H: 40S ribosomal protein S13 N-terminal domain (From Topology)	T: 40S ribosomal protein S13 N-terminal domain	F: Ribosomal_S13_N_1	ECOD (1.6)
P [auth Q]	Ribosomal_S15_2	e5jbhQ1	A: alpha arrays	X: S15/NS1 RNA-binding domain (From Topology)	H: S15/NS1 RNA-binding domain (From Topology)	T: S15/NS1 RNA-binding domain	F: Ribosomal_S15_2	ECOD (1.6)
Q [auth R]	Ribosomal_S17_1	e5jbhR1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Ribosomal_S17_1	ECOD (1.6)
R [auth A]	Ribosomal_S3Ae_N	e5jbhA1	A: beta barrels	X: Ribosomal protein L25-like	H: 40S ribosomal protein S3A N-terminal domain (From Topology)	T: 40S ribosomal protein S3A N-terminal domain	F: Ribosomal_S3Ae_N	ECOD (1.6)
R [auth A]	Ribosomal_S3Ae_C	e5jbhA2	A: a+b two layers	X: T-fold	H: 40S ribosomal protein S3A C-terminal domain (From Topology)	T: 40S ribosomal protein S3A C-terminal domain	F: Ribosomal_S3Ae_C	ECOD (1.6)
S [auth B]	Ribosomal_S2_2	e5jbhB1	A: a/b three-layered sandwiches	X: Flavodoxin-like	H: Ribosomal protein S2/SIS domain (From Topology)	T: Ribosomal protein S2/SIS domain	F: Ribosomal_S2_2	ECOD (1.6)
B [auth Z]	Ribosomal_S3_C	e5jbhZ2	A: a+b two layers	X: T-fold	H: Ribosomal protein S3-C (From Topology)	T: Ribosomal protein S3-C	F: Ribosomal_S3_C	ECOD (1.6)
B [auth Z]	KH_2_2	e5jbhZ1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: KH-domains	T: Prokaryotic type KH domain (KH-domain type II)	F: KH_2_2	ECOD (1.6)
T [auth V]	Ribosomal_S24e	e5jbhV1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal proteins S24e, L23 and L15e (From Topology)	T: Ribosomal proteins S24e, L23 and L15e	F: Ribosomal_S24e	ECOD (1.6)
U [auth W]	Ribosomal_S27e	e5jbhW1	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: Ribosomal_S27e	ECOD (1.6)
V [auth D]	S4	e5jbhD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: S4	ECOD (1.6)
W [auth E]	UNK_F_TYPE	e5jbhE2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: UNK_F_TYPE	ECOD (1.6)
W [auth E]	KOW_1	e5jbhE3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: KOW_1	ECOD (1.6)
W [auth E]	RS4NT	e5jbhE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Alpha-L RNA-binding motif	F: RS4NT	ECOD (1.6)
X [auth F]	Ribosomal_S5_C	e5jbhF3	A: a+b two layers	X: Ribosomal protein S5 domain 2-like (From Topology)	H: Ribosomal protein S5 domain 2-like (From Topology)	T: Ribosomal protein S5 domain 2-like	F: Ribosomal_S5_C	ECOD (1.6)
X [auth F]	Ribosomal_S5_2	e5jbhF2	A: extended segments	X: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)	H: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)	T: N-terminal region in 40S ribosomal protein rpS2 (S5p)	F: Ribosomal_S5_2	ECOD (1.6)
Y [auth G]	Ribosomal_S6e	e5jbhG1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_S6e	ECOD (1.6)
Z [auth I]	Ribosomal_S8_N_1	e5jbhI2	A: a+b two layers	X: R3H domain-like	H: Ribosomal protein S8, N-terminal domain (From Topology)	T: Ribosomal protein S8, N-terminal domain	F: Ribosomal_S8_N_1	ECOD (1.6)
Z [auth I]	Ribosomal_S8_C_1	e5jbhI1	A: a+b two layers	X: Ribosomal protein S8, C-terminal domain (From Topology)	H: Ribosomal protein S8, C-terminal domain (From Topology)	T: Ribosomal protein S8, C-terminal domain	F: Ribosomal_S8_C_1	ECOD (1.6)
AA [auth J]	Ribosomal_S8e	e5jbhJ1	A: beta barrels	X: Ribosomal protein L14-like	H: Ribosomal protein L14-related (From Topology)	T: Ribosomal protein L14-related	F: Ribosomal_S8e	ECOD (1.6)
CA [auth 0]	Ribosomal_L41_like	e5jbh01	A: extended segments	X: Ribosomal protein L41-A (From Topology)	H: Ribosomal protein L41-A (From Topology)	T: Ribosomal protein L41-A	F: Ribosomal_L41_like	ECOD (1.6)
C [auth 3]	Ribosomal_L7Ae_1	e5jbh31	A: a+b three layers	X: Bacillus chorismate mutase-like	H: L30e-like (From Topology)	T: L30e-like	F: Ribosomal_L7Ae_1	ECOD (1.6)
EA [auth 1]	SUI1	e5jbh11	A: a+b two layers	X: Glucose permease domain IIB-like	H: eIF1-like (From Topology)	T: eIF1-like	F: SUI1	ECOD (1.6)
GA [auth 6]	eIF-1a	e5jbh61	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: eIF-1a	ECOD (1.6)
HA [auth 7]	GTP_EFTU_D2_2	e5jbh73	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: GTP_EFTU_D2_2	ECOD (1.6)
HA [auth 7]	eIF2_C	e5jbh72	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Aminomethyltransferase beta-barrel domain	F: eIF2_C	ECOD (1.6)
HA [auth 7]	MnmE_helical_2nd	e5jbh71	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: MnmE_helical_2nd	ECOD (1.6)
HA [auth 7]	DUF35_N_like	e5jbh74	A: few secondary structure elements	X: Rubredoxin-like	H: Rubredoxin-related	T: Rubredoxin-related	F: DUF35_N_like	ECOD (1.6)
IA [auth 8]	eIF-5_eIF-2B_N	e5jbh82	A: alpha arrays	X: HTH	H: HTH	T: winged	F: eIF-5_eIF-2B_N	ECOD (1.6)
IA [auth 8]	eIF-5_eIF-2B_C	e5jbh81	A: few secondary structure elements	X: Rubredoxin-like	H: Zinc-binding domain of translation initiation factor 2 beta (From Topology)	T: Zinc-binding domain of translation initiation factor 2 beta	F: eIF-5_eIF-2B_C	ECOD (1.6)
JA [auth 9]	S1_1	e5jbh91	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: S1_1	ECOD (1.6)
JA [auth 9]	EIF_2_alpha_N_1	e5jbh92	A: alpha arrays	X: HhH/H2TH	H: eIF2alpha middle domain (From Topology)	T: eIF2alpha middle domain	F: EIF_2_alpha_N_1	ECOD (1.6)
JA [auth 9]	EIF_2_alpha_C_1	e5jbh93	A: a+b two layers	X: Alpha-beta plaits	H: eIF-2-alpha, C-terminal domain (From Topology)	T: eIF-2-alpha, C-terminal domain	F: EIF_2_alpha_C_1	ECOD (1.6)
D [auth L]	Ribosomal_S10_1	e5jbhL1	A: a+b two layers	X: Alpha-beta plaits	H: Ribosomal protein S10 (From Topology)	T: Ribosomal protein S10	F: Ribosomal_S10_1	ECOD (1.6)
E [auth O]	Ribosomal_S13	e5jbhO1	A: alpha arrays	X: HhH/H2TH	H: H2TH (From Topology)	T: H2TH	F: Ribosomal_S13	ECOD (1.6)
F [auth P]	Ribosomal_S14_2	e5jbhP1	A: few secondary structure elements	X: Glucocorticoid receptor-like	H: LIM domain-like	T: LIM domain-like	F: Ribosomal_S14_2	ECOD (1.6)
G [auth S]	Ribosomal_S17e	e5jbhS1	A: alpha arrays	X: HTH	H: HTH	T: FF domain	F: Ribosomal_S17e	ECOD (1.6)
H [auth T]	Ribosomal_S19	e5jbhT1	A: a+b two layers	X: Ribosomal protein S19 (From Topology)	H: Ribosomal protein S19 (From Topology)	T: Ribosomal protein S19	F: Ribosomal_S19	ECOD (1.6)
I [auth U]	Ribosomal_S19e	e5jbhU1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: Ribosomal_S19e	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Identifier	Description	Comments	Source
J [auth X]	PF01200	Ribosomal protein S28e (Ribosomal_S28e)	Ribosomal protein S28e	-	Family
K [auth Y]	PF01599	Ribosomal protein S27a (Ribosomal_S27)	Ribosomal protein S27a	This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins ...	This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis [3]. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [2].	Domain
L [auth H]	PF00177	Ribosomal protein S7p/S5e (Ribosomal_S7)	Ribosomal protein S7p/S5e	This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.	Domain
M [auth K]	PF00380	Ribosomal protein S9/S16 (Ribosomal_S9)	Ribosomal protein S9/S16	-	Family
N [auth M]	PF00411	Ribosomal protein S11 (Ribosomal_S11)	Ribosomal protein S11	-	Family
O [auth N]	PF00164	Ribosomal protein S12/S23 (Ribosom_S12_S23)	Ribosomal protein S12/S23	-	Family
P [auth Q]	PF08069	Ribosomal S13/S15 N-terminal domain (Ribosomal_S13_N)	Ribosomal S13/S15 N-terminal domain	This domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1].	Domain
P [auth Q]	PF00312	Ribosomal protein S15 (Ribosomal_S15)	Ribosomal protein S15	-	Domain
Q [auth R]	PF00366	Ribosomal protein S17 (Ribosomal_S17)	Ribosomal protein S17	-	Domain
R [auth A]	PF01015	Ribosomal S3Ae family (Ribosomal_S3Ae)	Ribosomal S3Ae family	-	Family
S [auth B]	PF00318	Ribosomal protein S2 (Ribosomal_S2)	Ribosomal protein S2	-	Family
B [auth Z]	PF07650	KH domain (KH_2)	KH domain	-	Domain
B [auth Z]	PF00189	Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)	Ribosomal protein S3, C-terminal domain	This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.	Domain
T [auth V]	PF01282	Ribosomal protein S24e (Ribosomal_S24e)	Ribosomal protein S24e	-	Family
U [auth W]	PF01667	Ribosomal protein S27 (Ribosomal_S27e)	Ribosomal protein S27	-	Family
V [auth D]	PF01479	S4 domain (S4)	S4 domain	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.	Domain
W [auth E]	PF00900	Ribosomal family S4e (Ribosomal_S4e)	Ribosomal family S4e	-	Family
W [auth E]	PF08071	RS4NT (NUC023) domain (RS4NT)	RS4NT (NUC023) domain	This is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1].	Domain
W [auth E]	PF01479	S4 domain (S4)	S4 domain	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast pro ...	The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA.	Domain
X [auth F]	PF03719	Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)	Ribosomal protein S5, C-terminal domain	-	Domain
X [auth F]	PF00333	Ribosomal protein S5, N-terminal domain (Ribosomal_S5)	Ribosomal protein S5, N-terminal domain	-	Domain
Y [auth G]	PF01092	Ribosomal protein S6e (Ribosomal_S6e)	Ribosomal protein S6e	-	Family
Z [auth I]	PF00410	Ribosomal protein S8 (Ribosomal_S8)	Ribosomal protein S8	-	Domain
AA [auth J]	PF01201	Ribosomal protein S8e (Ribosomal_S8e)	Ribosomal protein S8e	-	Family
C [auth 3]	PF01248	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)	Ribosomal protein L7Ae/L30e/S12e/Gadd45 family	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...	This family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD118 [1].	Domain
EA [auth 1]	PF01253	Translation initiation factor SUI1 (SUI1)	Translation initiation factor SUI1	-	Domain
GA [auth 6]	PF01176	Translation initiation factor 1A / IF-1 (eIF-1a)	Translation initiation factor 1A / IF-1	This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.	Domain
HA [auth 7]	PF00009	Elongation factor Tu GTP binding domain (GTP_EFTU)	Elongation factor Tu GTP binding domain	This domain contains a P-loop motif, also found in several other families such as Pfam:PF00071, Pfam:PF00025 and Pfam:PF00063. Elongation factor Tu consists of three structural domains, this plus two C-terminal beta barrel domains.	Domain
HA [auth 7]	PF09173	Initiation factor eIF2 gamma, C terminal (eIF2_C)	Initiation factor eIF2 gamma, C terminal	Members of this family, which are found in the initiation factors eIF2 and EF-Tu, adopt a structure consisting of a beta barrel with Greek key topology. They are required for formation of the ternary complex with GTP and initiator tRNA [1].	Domain
HA [auth 7]	PF03144	Elongation factor Tu domain 2 (GTP_EFTU_D2)	Elongation factor Tu domain 2	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as e ...	Elongation factor Tu consists of three structural domains, this is the second domain. This domain adopts a beta barrel structure. This the second domain is involved in binding to charged tRNA [1]. This domain is also found in other proteins such as elongation factor G and translation initiation factor IF-2. This domain is structurally related to Pfam:PF03143, and in fact has weak sequence matches to this domain.	Domain
IA [auth 8]	PF01873	Domain found in IF2B/IF5 (eIF-5_eIF-2B)	Domain found in IF2B/IF5	-	Family
JA [auth 9]	PF07541	Eukaryotic translation initiation factor 2 alpha subunit (EIF_2_alpha)	Eukaryotic translation initiation factor 2 alpha subunit	-	Family
JA [auth 9]	PF00575	S1 RNA binding domain (S1)	S1 RNA binding domain	The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.	Domain
D [auth L]	PF00338	Ribosomal protein S10p/S20e (Ribosomal_S10)	Ribosomal protein S10p/S20e	This family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.	Domain
E [auth O]	PF00416	Ribosomal protein S13/S18 (Ribosomal_S13)	Ribosomal protein S13/S18	-	Family
F [auth P]	PF00253	Ribosomal protein S14p/S29e (Ribosomal_S14)	Ribosomal protein S14p/S29e	-	Family
G [auth S]	PF00833	Ribosomal S17 (Ribosomal_S17e)	Ribosomal S17	-	Family
H [auth T]	PF00203	Ribosomal protein S19 (Ribosomal_S19)	Ribosomal protein S19	-	Domain
I [auth U]	PF01090	Ribosomal protein S19e (Ribosomal_S19e)	Ribosomal protein S19e	-	Family

Gene Product Annotation Gene Product Annotation

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth 2]	16S ribosomal RNA	none	none	none
J [auth X]	30S ribosomal protein eS28	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
K [auth Y]	30S ribosomal protein eS27	structural constituent of ribosome structural molecule activity binding zinc ion binding ion binding cation binding metal ion binding transition metal ion binding		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
L [auth H]	30S ribosomal protein uS7	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
M [auth K]	30S ribosomal protein uS9	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
N [auth M]	30S ribosomal protein uS11	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
O [auth N]	30S ribosomal protein uS12	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
P [auth Q]	30S ribosomal protein uS15	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
Q [auth R]	30S ribosomal protein uS17	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
R [auth A]	30S ribosomal protein uS3	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
S [auth B]	30S ribosomal protein uS2	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
B [auth Z]	30S ribosomal protein uS3	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
T [auth V]	30S ribosomal protein eS24	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
U [auth W]	30S ribosomal protein eS27	structural constituent of ribosome structural molecule activity binding zinc ion binding ion binding cation binding metal ion binding transition metal ion binding		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
V [auth D]	30S ribosomal protein uS4	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
W [auth E]	30S ribosomal protein eS4	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
X [auth F]	30S ribosomal protein uS5	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
Y [auth G]	30S ribosomal protein eS6	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
Z [auth I]	30S ribosomal protein uS8	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
AA [auth J]	30S ribosomal protein eS8	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
BA [auth C]	30S ribosomal protein SX	none	none	none
CA [auth 0]	30S ribosomal protein eL41			intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
C [auth 3]	50S ribosomal protein uL30	catalytic activity nuclease activity endonuclease activity RNA endonuclease activity ribonuclease P activity RNA nuclease activity tRNA-specific ribonuclease activity hydrolase activity hydrolase activity, acting on ester bonds RNA endonuclease activity, producing 5'-phosphomonoesters endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters catalytic activity, acting on RNA catalytic activity, acting on a tRNA catalytic activity, acting on a nucleic acid nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity	cellular process ribonucleoprotein complex biogenesis ribosome biogenesis cellular component biogenesis cellular component organization or biogenesis	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex ribonucleoprotein complex ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle
DA [auth 5]	mRNA	none	none	none
EA [auth 1]	aIF1	nucleic acid binding RNA binding mRNA binding binding organic cyclic compound binding heterocyclic compound binding translation initiation factor activity translation factor activity, RNA binding translation regulator activity translation regulator activity, nucleic acid binding
FA [auth 4]	initiator Met-tRNA fMet from E. coli (A1U72 variant)	none	none	none
GA [auth 6]	aIF1A	nucleic acid binding RNA binding binding organic cyclic compound binding heterocyclic compound binding translation initiation factor activity translation factor activity, RNA binding translation regulator activity translation regulator activity, nucleic acid binding
HA [auth 7]	aIF2-gamma	catalytic activity GTPase activity pyrophosphatase activity hydrolase activity hydrolase activity, acting on acid anhydrides hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides ribonucleoside triphosphate phosphatase activity binding ion binding cation binding metal ion binding nucleic acid binding translation elongation factor activity translation factor activity, RNA binding translation regulator activity translation regulator activity, nucleic acid binding organic cyclic compound binding heterocyclic compound binding translation initiation factor activity
IA [auth 8]	aIF2-beta	nucleic acid binding translation initiation factor activity binding translation factor activity, RNA binding translation regulator activity translation regulator activity, nucleic acid binding organic cyclic compound binding heterocyclic compound binding
JA [auth 9]	aIF2-alpha	binding ribonucleoprotein complex binding ribosome binding protein-containing complex binding nucleic acid binding RNA binding organic cyclic compound binding heterocyclic compound binding translation initiation factor activity translation factor activity, RNA binding translation regulator activity translation regulator activity, nucleic acid binding
D [auth L]	30S ribosomal protein uS10	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
E [auth O]	30S ribosomal protein uS13	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
F [auth P]	30S ribosomal protein uS14	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity zinc ion binding ion binding cation binding metal ion binding transition metal ion binding		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
G [auth S]	30S ribosomal protein eS17	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity
H [auth T]	30S ribosomal protein uS19	nucleic acid binding RNA binding binding rRNA binding organic cyclic compound binding heterocyclic compound binding structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome small ribosomal subunit protein-containing complex organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle ribosomal subunit cellular anatomical entity ribonucleoprotein complex
I [auth U]	30S ribosomal protein eS19	structural constituent of ribosome structural molecule activity		intracellular anatomical structure ribosome organelle non-membrane-bounded organelle intracellular organelle intracellular non-membrane-bounded organelle cellular anatomical entity

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.

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5JBH

Cryo-EM structure of a full archaeal ribosomal translation initiation complex in the P-IN conformation

Present annotations:

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Product Annotation Gene Product Annotation