5JBH

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


Protein Family Annotation Pfam Database Homepage

ChainsAccessionIdentifierDescriptionCommentsSource
PF01248Ribosomal 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
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00833Ribosomal S17 (Ribosomal_S17e)Ribosomal S17- Family
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF01599Ribosomal 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
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF01015Ribosomal S3Ae family (Ribosomal_S3Ae)Ribosomal S3Ae family- Family
PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
PF01479S4 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
PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
PF01253Translation initiation factor SUI1 (SUI1)Translation initiation factor SUI1- Domain
PF07541Eukaryotic translation initiation factor 2 alpha subunit (EIF_2_alpha)Eukaryotic translation initiation factor 2 alpha subunit- Family
PF00575S1 RNA binding domain (S1)S1 RNA binding domainThe 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
PF01200Ribosomal protein S28e (Ribosomal_S28e)Ribosomal protein S28e- Family
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF08069Ribosomal 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
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
PF07650KH domain (KH_2)KH domain- Domain
PF00189Ribosomal protein S3, C-terminal domain (Ribosomal_S3_C)Ribosomal protein S3, C-terminal domainThis 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
PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
PF08071RS4NT (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
PF01479S4 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
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
PF01176Translation initiation factor 1A / IF-1 (eIF-1a)Translation initiation factor 1A / IF-1This family includes both the eukaryotic translation factor eIF-1A and the bacterial translation initiation factor IF-1.Domain
PF00009Elongation factor Tu GTP binding domain (GTP_EFTU)Elongation factor Tu GTP binding domainThis 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
PF03144Elongation factor Tu domain 2 (GTP_EFTU_D2)Elongation factor Tu domain 2Elongation 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
PF09173Initiation factor eIF2 gamma, C terminal (eIF2_C)Initiation factor eIF2 gamma, C terminalMembers 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
PF01873Domain found in IF2B/IF5 (eIF-5_eIF-2B)Domain found in IF2B/IF5- Family
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family

Gene Product Annotation Gene Product Annotation

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
50S ribosomal protein uL30
30S ribosomal protein uS10
    30S ribosomal protein uS13
      30S ribosomal protein eS17
        30S ribosomal protein uS19
          30S ribosomal protein eS27
            30S ribosomal protein uS9
              30S ribosomal protein uS3
                30S ribosomal protein eS24
                  30S ribosomal protein eS27
                    30S ribosomal protein uS4
                      30S ribosomal protein uS5
                        30S ribosomal protein eS6
                          30S ribosomal protein SXnonenonenone
                          aIF1
                              aIF2-alpha
                                  16S ribosomal RNAnonenonenone
                                  30S ribosomal protein eS28
                                    30S ribosomal protein uS7
                                      30S ribosomal protein uS11
                                        30S ribosomal protein uS12
                                          30S ribosomal protein uS15
                                            30S ribosomal protein uS17
                                              30S ribosomal protein uS2
                                                30S ribosomal protein uS3
                                                  30S ribosomal protein eS4
                                                    30S ribosomal protein uS8
                                                      30S ribosomal protein eS8
                                                        30S ribosomal protein eL41
                                                            mRNAnonenonenone
                                                            initiator Met-tRNA fMet from E. coli (A1U72 variant)nonenonenone
                                                            aIF1A
                                                                aIF2-gamma
                                                                  aIF2-beta
                                                                      30S ribosomal protein uS14
                                                                        30S ribosomal protein eS19