6EML

Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae


ChainDomainClassArchitectureTopologyHomology
J2.40.50.140 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
L3.40.50.10490 Alpha Beta 3-Layer(aba) Sandwich Rossmann fold Glucose-6-phosphate isomerase like protein
N3.30.160.20 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
N3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
O3.10.290.10 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region Chain A
O2.40.50.740 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Ribosomal protein S4, central domain
O2.30.30.30 Mainly Beta Roll SH3 type barrels.
R1.10.168.20 Mainly Alpha Orthogonal Bundle Phosducin domain 2
B3.30.1330.30 Alpha Beta 2-Layer Sandwich 60s Ribosomal Protein L30 Chain: A
T2.40.50.1000 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P)
U1.10.287.10 Mainly Alpha Orthogonal Bundle Helix Hairpins S15/NS1, RNA-binding
V3.30.420.80 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase domain 5
W3.30.1230.20 Alpha Beta 2-Layer Sandwich Hypothetical Cytosolic Protein Chain: A
X3.30.1370.30 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8 Chain: A, domain 1
X3.30.1490.10 Alpha Beta 2-Layer Sandwich Dna Ligase domain 1
Z3.30.70.3370 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
AA2.20.25.100 Mainly Beta Single Sheet N-terminal domain of TfIIb Ribosomal protein S27
C1.10.455.10 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal protein S7/S5
F3.30.230.10 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5 domain 2
I1.10.10.10 Mainly Alpha Orthogonal Bundle Arc Repressor Mutant, subunit A Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain

Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
JPF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
KPF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].
Domain
KPF01599Ribosomal protein S27a (Ribosomal_S27)Ribosomal protein S27aThis 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
LPF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
MPF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
NPF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
NPF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
OPF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
OPF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
OPF08071RS4NT (NUC023) domain (RS4NT)RS4NT (NUC023) domainThis is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1].Domain
OPF01479S4 domain (S4)S4 domainThe 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
OPF00467KOW motif (KOW)KOW motif- Family
PPF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
QPF01251Ribosomal protein S7e (Ribosomal_S7e)Ribosomal protein S7e- Family
RPF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
SPF01479S4 domain (S4)S4 domainThe 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
BPF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis 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
TPF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
TPF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
UPF08069Ribosomal S13/S15 N-terminal domain (Ribosomal_S13_N)Ribosomal S13/S15 N-terminal domainThis domain is found at the N-terminus of ribosomal S13 and S15 proteins. This domain is also identified as NUC021 [1].Domain
UPF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
VPF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
WPF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
XPF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
YPF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
ZPF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
AAPF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
BAPF08142AARP2CN (NUC121) domain (AARP2CN)AARP2CN (NUC121) domainThis domain is the central domain of AARP2. It is weakly similar to the GTP-binding domain of elongation factor TU [1].Domain
BAPF0495040S ribosome biogenesis protein Tsr1 and BMS1 C-terminal (RIBIOP_C)40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal- Family
CAPF04758Ribosomal protein S30 (Ribosomal_S30)Ribosomal protein S30- Family
CPF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
DAPF17903Krr1 KH1 domain (KH_8)Krr1 KH1 domainThis entry represents the first KH domain in the KRR1 protein [1]. Krr1 is a ribosomal assembly factor. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1 [1].Domain
EAPF09202Rio2, N-terminal (Rio2_N)Rio2, N-terminalMembers of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding ...Members of this family are found in Rio2, and are structurally homologous to the winged helix (wHTH) domain. They adopt a structure consisting of four alpha helices followed by two beta strands and a fifth alpha helix. The domain confers DNA binding properties to the protein, as per other winged helix domains [1].
Domain
FAPF05291Bystin (Bystin)Bystin- Family
DPF00833Ribosomal S17 (Ribosomal_S17e)Ribosomal S17- Family
EPF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
FPF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
GPF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
HPF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
IPF03297S25 ribosomal protein (Ribosomal_S25)S25 ribosomal protein- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
2pre-18S ribosomal RNAnone none none
L40S ribosomal protein S28-B
NUbiquitin-40S ribosomal protein S31
P40S ribosomal protein S0-A
Q40S ribosomal protein S1-A
R40S ribosomal protein S2
S40S ribosomal protein S4-A
T40S ribosomal protein S6-A
U40S ribosomal protein S7-A
V40S ribosomal protein S8-A
W40S ribosomal protein S9-A
D40S ribosomal protein S12
X40S ribosomal protein S11-A
Y40S ribosomal protein S13
Z40S ribosomal protein S14-A
a40S ribosomal protein S21-A
b40S ribosomal protein S22-A
c40S ribosomal protein S23-A
d40S ribosomal protein S24-A
f40S ribosomal protein S27-A
tRibosome biogenesis protein TSR1
g40S ribosomal protein S30-A
B40S ribosomal protein S5
pPre-rRNA-processing protein PNO1
rSerine/threonine-protein kinase RIO2
eEssential nuclear protein 1
C40S ribosomal protein S17-A
E40S ribosomal protein S15
F40S ribosomal protein S16-A
H40S ribosomal protein S18-A
I40S ribosomal protein S19-A
K40S ribosomal protein S25-A