6SWD | pdb_00006swd

IC2 body model of cryo-EM structure of a full archaeal ribosomal translation initiation complex devoid of aIF1 in P. abyssi


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ISCOP2B SuperfamilyRibosomal protein S8 8094002 3000709 SCOP2B (2022-06-29)
H [auth G]SCOP2B SuperfamilyGS N-terminal domain-like 8093818 3000408 SCOP2B (2022-06-29)
C [auth B]SCOP2B SuperfamilySIS domain/Ribosomal protein S2-like 8093792 3001397 SCOP2B (2022-06-29)
B [auth A]SCOP2B SuperfamilyRibosomal S3Ae-like 8094349 3002166 SCOP2B (2022-06-29)
S [auth 6]SCOP2B SuperfamilyNucleic acid-binding proteins 8085842 3000135 SCOP2B (2022-06-29)
P [auth W]SCOP2B SuperfamilyZn-binding ribosomal proteins 8095129 3001320 SCOP2B (2022-06-29)
O [auth V]SCOP2B SuperfamilyRibosomal proteins S24e, L23 and L15e 8037389 3000210 SCOP2B (2022-06-29)
K [auth M]SCOP2B SuperfamilyTranslational machinery components 8098828 3000571 SCOP2B (2022-06-29)
JSCOP2B Superfamily50S Ribosomal protein L14-like 8093764 3000433 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
IRibosomal_S8_N_1e6swdI1 A: a+b two layersX: R3H domain-likeH: Ribosomal protein S8, N-terminal domain (From Topology)T: Ribosomal protein S8, N-terminal domainF: Ribosomal_S8_N_1ECOD (1.6)
IRibosomal_S8_C_1e6swdI2 A: a+b two layersX: Ribosomal protein S8, C-terminal domain (From Topology)H: Ribosomal protein S8, C-terminal domain (From Topology)T: Ribosomal protein S8, C-terminal domainF: Ribosomal_S8_C_1ECOD (1.6)
H [auth G]Ribosomal_S6ee6swdG1 A: beta barrelsX: Ribosomal protein L25-likeH: Ribosomal protein L25-like (From Topology)T: Ribosomal protein L25-likeF: Ribosomal_S6eECOD (1.6)
F [auth E]UNK_F_TYPEe6swdE3 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: UNK_F_TYPEECOD (1.6)
F [auth E]KOW_1e6swdE1 A: beta barrelsX: SH3H: SH3T: SH3F: KOW_1ECOD (1.6)
F [auth E]RS4NTe6swdE2 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: RS4NTECOD (1.6)
E [auth D]S4e6swdD1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: S4ECOD (1.6)
D [auth C]zf-C2H2_19e6swdC1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: zf-C2H2_19ECOD (1.6)
C [auth B]Ribosomal_S2_2e6swdB1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Ribosomal protein S2/SIS domain (From Topology)T: Ribosomal protein S2/SIS domainF: Ribosomal_S2_2ECOD (1.6)
B [auth A]Ribosomal_S3Ae_Ne6swdA1 A: beta barrelsX: Ribosomal protein L25-likeH: 40S ribosomal protein S3A N-terminal domain (From Topology)T: 40S ribosomal protein S3A N-terminal domainF: Ribosomal_S3Ae_NECOD (1.6)
B [auth A]Ribosomal_S3Ae_Ce6swdA2 A: a+b two layersX: T-foldH: 40S ribosomal protein S3A C-terminal domain (From Topology)T: 40S ribosomal protein S3A C-terminal domainF: Ribosomal_S3Ae_CECOD (1.6)
S [auth 6]eIF-1ae6swd61 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: eIF-1aECOD (1.6)
Q [auth 0]Ribosomal_L41_2e6swd01 A: extended segmentsX: Ribosomal protein L41-A (From Topology)H: Ribosomal protein L41-A (From Topology)T: Ribosomal protein L41-AF: Ribosomal_L41_2ECOD (1.6)
P [auth W]Ribosomal_S27ee6swdW1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_S27eECOD (1.6)
O [auth V]Ribosomal_S24ee6swdV1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal proteins S24e, L23 and L15e (From Topology)T: Ribosomal proteins S24e, L23 and L15eF: Ribosomal_S24eECOD (1.6)
N [auth R]Ribosomal_S17_1e6swdR1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_S17_1ECOD (1.6)
M [auth Q]Ribosomal_S13_N_1e6swdQ2 A: alpha arraysX: HTHH: 40S ribosomal protein S13 N-terminal domain (From Topology)T: 40S ribosomal protein S13 N-terminal domainF: Ribosomal_S13_N_1ECOD (1.6)
M [auth Q]Ribosomal_S15_2e6swdQ1 A: alpha arraysX: S15/NS1 RNA-binding domain (From Topology)H: S15/NS1 RNA-binding domain (From Topology)T: S15/NS1 RNA-binding domainF: Ribosomal_S15_2ECOD (1.6)
L [auth N]Ribosom_S12_S23e6swdN1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosom_S12_S23ECOD (1.6)
K [auth M]Ribosomal_S11e6swdM1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_S11ECOD (1.6)
JRibosomal_S8ee6swdJ1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: Ribosomal_S8eECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
30S ribosomal protein S8
H [auth G]30S ribosomal protein S6e
G [auth F]30S ribosomal protein S5
F [auth E]30S ribosomal protein S4e
E [auth D]30S ribosomal protein S4
D [auth C]Zn-ribbon RNA-binding protein involved in translation- - -
C [auth B]30S ribosomal protein S2
B [auth A]30S ribosomal protein S3Ae
S [auth 6]Translation initiation factor 1A - -
R [auth 5]mRNA---
Q [auth 0]30S ribosomal protein aL41- -
P [auth W]30S ribosomal protein S27e
O [auth V]30S ribosomal protein S24e
N [auth R]30S ribosomal protein S17
M [auth Q]30S ribosomal protein S15
L [auth N]30S ribosomal protein S12
K [auth M]30S ribosomal protein S11
30S ribosomal protein S8e
A [auth 2]16S ribosomal RNA---

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR000630Small ribosomal subunit protein uS8Family
IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
H [auth G]IPR001377Small ribosomal subunit protein eS6Family
H [auth G]IPR018282Small ribosomal subunit protein eS6, conserved siteConserved Site
H [auth G]IPR020924Small ribosomal subunit protein eS6, archaeaFamily
G [auth F]IPR005711Small ribosomal subunit protein uS5, eukaryota_archaeaFamily
G [auth F]IPR000851Small ribosomal subunit protein uS5Family
G [auth F]IPR047866Small ribosomal subunit protein uS5, archaeaFamily
G [auth F]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
G [auth F]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
G [auth F]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
G [auth F]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
G [auth F]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
F [auth E]IPR018199Small ribosomal subunit protein eS4, N-terminal, conserved siteConserved Site
F [auth E]IPR013843Small ribosomal subunit protein eS4, N-terminalDomain
F [auth E]IPR002942RNA-binding S4 domainDomain
F [auth E]IPR013845Small ribosomal subunit protein eS4, central regionDomain
F [auth E]IPR000876Small ribosomal subunit protein eS4Family
F [auth E]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
F [auth E]IPR038237Small ribosomal subunit protein eS4, central domain superfamilyHomologous Superfamily
F [auth E]IPR041982Small ribosomal subunit protein eS4, KOW domainDomain
F [auth E]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
F [auth E]IPR005824KOWDomain
E [auth D]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
E [auth D]IPR002942RNA-binding S4 domainDomain
E [auth D]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
E [auth D]IPR022802Small ribosomal subunit protein uS4, archaeaFamily
E [auth D]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
E [auth D]IPR022801Small ribosomal subunit protein uS4Family
E [auth D]IPR005710Small ribosomal subunit protein uS4, eukaryota/archaeaFamily
D [auth C]IPR011668Ribosomal protein aS21, zinc-binding pocketDomain
D [auth C]IPR044720Zinc finger protein HVO_2753-likeFamily
C [auth B]IPR023454Small ribosomal subunit protein uS2, archaeaFamily
C [auth B]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
C [auth B]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
C [auth B]IPR001865Small ribosomal subunit protein uS2Family
C [auth B]IPR005707Small ribosomal subunit protein uS2, eukaryota/archaeaFamily
B [auth A]IPR001593Small ribosomal subunit protein eS1Family
B [auth A]IPR018281Small ribosomal subunit protein eS1, conserved siteConserved Site
B [auth A]IPR030838Small ribosomal subunit protein eS1, archaeaFamily
S [auth 6]IPR018104Translation initiation factor 1A (eIF-1A), conserved siteConserved Site
S [auth 6]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
S [auth 6]IPR006196RNA-binding domain, S1, IF1 typeDomain
S [auth 6]IPR001253Translation initiation factor 1A (eIF-1A)Family
P [auth W]IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
P [auth W]IPR000592Small ribosomal subunit protein eS27Family
P [auth W]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
O [auth V]IPR001976Small ribosomal subunit protein eS24Family
O [auth V]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
O [auth V]IPR012677Nucleotide-binding alpha-beta plait domain superfamilyHomologous Superfamily
O [auth V]IPR018098Small ribosomal subunit protein eS24 conserved siteConserved Site
N [auth R]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
N [auth R]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
N [auth R]IPR000266Small ribosomal subunit protein uS17Family
N [auth R]IPR019978Small ribosomal subunit protein uS17, archaealFamily
N [auth R]IPR028333Small ribosomal subunit protein uS17, archaeal/eukaryoticFamily
M [auth Q]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
M [auth Q]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
M [auth Q]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotaFamily
M [auth Q]IPR000589Small ribosomal subunit protein uS15Family
L [auth N]IPR006032Small ribosomal subunit protein uS12Family
L [auth N]IPR022863Ribosomal protein uS12, archaeaFamily
L [auth N]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
L [auth N]IPR005680Small ribosomal subunit protein uS12, eukaryota/archaeaFamily
K [auth M]IPR019961Small ribosomal subunit protein uS11, archaeaFamily
K [auth M]IPR001971Small ribosomal subunit protein uS11Family
K [auth M]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
K [auth M]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
IPR001047Small ribosomal subunit protein eS8Family
IPR020919Small ribosomal subunit protein eS8, archaeaFamily
IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
IPR018283Small ribosomal subunit protein eS8, conserved siteConserved Site