5NO4

RsgA-GDPNP bound to the 30S ribosomal subunit (RsgA assembly intermediate with uS3)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
C [auth D]SCOP2B SuperfamilyAlpha-L RNA-binding motif8083400 3001473 SCOP2B (2022-06-29)
L [auth M]SCOP2B SuperfamilyS13-like H2TH domain8098358 3000053 SCOP2B (2022-06-29)
J [auth K]SCOP2B SuperfamilyTranslational machinery components8035368 3000571 SCOP2B (2022-06-29)
M [auth N]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain)8052568 3000068 SCOP2B (2022-06-29)
N [auth O]SCOP2B SuperfamilyS15/NS1 RNA-binding domain8032375 3001284 SCOP2B (2022-06-29)
O [auth P]SCOP2B SuperfamilyRibosomal protein S168106547 3000680 SCOP2B (2022-06-29)
P [auth Q]SCOP2B SuperfamilyNucleic acid-binding proteins8059276 3000135 SCOP2B (2022-06-29)
R [auth S]SCOP2B SuperfamilyRibosomal protein S198103915 3000686 SCOP2B (2022-06-29)
E [auth F]SCOP2B SuperfamilyRibosomal protein S68066495 3001323 SCOP2B (2022-06-29)
G [auth H]SCOP2B SuperfamilyRibosomal protein S88079059 3000709 SCOP2B (2022-06-29)
H [auth I]SCOP2B SuperfamilyRibosomal protein S5 domain 2-like8082661 3000100 SCOP2B (2022-06-29)
I [auth J]SCOP2B SuperfamilyRibosomal protein S108102681 3001336 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
C [auth D]S4e5no4D1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: S4ECOD (1.6)
L [auth M]Ribosomal_S13_1e5no4M1 A: alpha arraysX: HhH/H2THH: H2TH (From Topology)T: H2THF: Ribosomal_S13_1ECOD (1.6)
S [auth T]Ribosomal_S20pe5no4T1 A: alpha bundlesX: Spectrin repeat-likeH: Ribosomal protein S20 (From Topology)T: Ribosomal protein S20F: Ribosomal_S20pECOD (1.6)
J [auth K]Ribosomal_S11e5no4K1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_S11ECOD (1.6)
M [auth N]Ribosomal_S14_1e5no4N1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: Ribosomal_S14_1ECOD (1.6)
N [auth O]Ribosomal_S15_1e5no4O1 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_1ECOD (1.6)
O [auth P]Ribosomal_S16e5no4P1 A: a+b two layersX: Ribosomal protein S16 (From Topology)H: Ribosomal protein S16 (From Topology)T: Ribosomal protein S16F: Ribosomal_S16ECOD (1.6)
P [auth Q]Ribosomal_S17_1e5no4Q1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_S17_1ECOD (1.6)
Q [auth R]Ribosomal_S18e5no4R1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: Ribosomal_S18ECOD (1.6)
R [auth S]Ribosomal_S19e5no4S1 A: a+b two layersX: Ribosomal protein S19 (From Topology)H: Ribosomal protein S19 (From Topology)T: Ribosomal protein S19F: Ribosomal_S19ECOD (1.6)
B [auth C]Ribosomal_S3_Ce5no4C1 A: a+b two layersX: T-foldH: Ribosomal protein S3-C (From Topology)T: Ribosomal protein S3-CF: Ribosomal_S3_CECOD (1.6)
B [auth C]KH_2_1e5no4C2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: KH-domainsT: Prokaryotic type KH domain (KH-domain type II)F: KH_2_1ECOD (1.6)
T [auth Z]RsgA_Ne5no4Z1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: RsgA_NECOD (1.6)
T [auth Z]RsgA_GTPasee5no4Z2 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: RsgA_GTPaseECOD (1.6)
D [auth E]Ribosomal_S5_Ce5no4E1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: Ribosomal_S5_CECOD (1.6)
D [auth E]Ribosomal_S5e5no4E2 A: a+b two layersX: dsRBD-likeH: dsRNA-binding domain-like (From Topology)T: dsRNA-binding domain-likeF: Ribosomal_S5ECOD (1.6)
E [auth F]Ribosomal_S6e5no4F1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S6 (From Topology)T: Ribosomal protein S6F: Ribosomal_S6ECOD (1.6)
F [auth G]Ribosomal_S7e5no4G1 A: alpha arraysX: Ribosomal protein S7 (From Topology)H: Ribosomal protein S7 (From Topology)T: Ribosomal protein S7F: Ribosomal_S7ECOD (1.6)
G [auth H]Ribosomal_S8_Ne5no4H1 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_NECOD (1.6)
G [auth H]Ribosomal_S8_Ce5no4H2 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_CECOD (1.6)
H [auth I]Ribosomal_S9e5no4I1 A: a+b two layersX: Ribosomal protein S5 domain 2-like (From Topology)H: Ribosomal protein S5 domain 2-like (From Topology)T: Ribosomal protein S5 domain 2-likeF: Ribosomal_S9ECOD (1.6)
I [auth J]Ribosomal_S10e5no4J1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S10 (From Topology)T: Ribosomal protein S10F: Ribosomal_S10ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
C [auth D]PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
C [auth D]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
L [auth M]PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
S [auth T]PF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
J [auth K]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
K [auth L]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
M [auth N]PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
N [auth O]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
O [auth P]PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
P [auth Q]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
Q [auth R]PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
R [auth S]PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
B [auth C]PF07650KH domain (KH_2)KH domain- Domain
B [auth C]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
T [auth Z]PF03193RsgA GTPase (RsgA_GTPase)RsgA GTPaseRsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular per ...RsgA (also known as EngC and YjeQ) represents a protein family whose members are broadly conserved in bacteria and are indispensable for growth. The GTPase domain of RsgA is very similar to several P-loop GTPases, but differs in having a circular permutation of the GTPase structure described by a G4-G1-G3 pattern [1].
Domain
D [auth E]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
D [auth E]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
E [auth F]PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
F [auth G]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
G [auth H]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
H [auth I]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
I [auth J]PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
16S ribosomal RNA---
C [auth D]30S ribosomal protein S4
L [auth M]30S ribosomal protein S13
S [auth T]30S ribosomal protein S20
J [auth K]30S ribosomal protein S11
K [auth L]30S ribosomal protein S12
M [auth N]30S ribosomal protein S14
N [auth O]30S ribosomal protein S15
O [auth P]30S ribosomal protein S16
P [auth Q]30S ribosomal protein S17
Q [auth R]30S ribosomal protein S18
R [auth S]30S ribosomal protein S19
B [auth C]30S ribosomal protein S3
T [auth Z]Small ribosomal subunit biogenesis GTPase RsgA
D [auth E]30S ribosomal protein S5
E [auth F]30S ribosomal protein S6
F [auth G]30S ribosomal protein S7
G [auth H]30S ribosomal protein S8
H [auth I]30S ribosomal protein S9
I [auth J]30S ribosomal protein S10

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
C [auth D]IPR002942RNA-binding S4 domainDomain
C [auth D]IPR005709Small ribosomal subunit protein uS4, bacterial-typeFamily
C [auth D]IPR022801Small ribosomal subunit protein uS4Family
C [auth D]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
C [auth D]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
C [auth D]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
L [auth M]IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
L [auth M]IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
L [auth M]IPR001892Small ribosomal subunit protein uS13Family
L [auth M]IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
L [auth M]IPR019980Small ribosomal subunit protein uS13, bacterial-typeFamily
S [auth T]IPR036510Small ribosomal subunit protein bS20 superfamilyHomologous Superfamily
S [auth T]IPR002583Small ribosomal subunit protein bS20Family
J [auth K]IPR001971Small ribosomal subunit protein uS11Family
J [auth K]IPR019981Small ribosomal subunit protein uS11, bacterial-typeFamily
J [auth K]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
J [auth K]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
K [auth L]IPR005679Ribosomal protein uS12, bacterial-typeFamily
K [auth L]IPR006032Small ribosomal subunit protein uS12Family
K [auth L]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
M [auth N]IPR001209Small ribosomal subunit protein uS14Family
M [auth N]IPR018271Small ribosomal subunit protein uS14, conserved siteConserved Site
M [auth N]IPR023036Small ribosomal subunit protein uS14, bacteria/plastidFamily
N [auth O]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
N [auth O]IPR000589Small ribosomal subunit protein uS15Family
N [auth O]IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
O [auth P]IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
O [auth P]IPR000307Small ribosomal subunit protein bS16Family
O [auth P]IPR020592Small ribosomal subunit protein bS16, conserved siteConserved Site
P [auth Q]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
P [auth Q]IPR019984Small ribosomal subunit protein uS17, bacteria/chloroplastFamily
P [auth Q]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
P [auth Q]IPR000266Small ribosomal subunit protein uS17Family
Q [auth R]IPR001648Small ribosomal subunit protein bS18Family
Q [auth R]IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
Q [auth R]IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
R [auth S]IPR002222Small ribosomal subunit protein uS19Family
R [auth S]IPR005732Small ribosomal subunit protein uS19, bacterial-typeFamily
R [auth S]IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
R [auth S]IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
B [auth C]IPR001351Small ribosomal subunit protein uS3, C-terminalDomain
B [auth C]IPR009019K homology domain superfamily, prokaryotic typeHomologous Superfamily
B [auth C]IPR004087K Homology domainDomain
B [auth C]IPR004044K Homology domain, type 2Domain
B [auth C]IPR015946K homology domain-like, alpha/betaHomologous Superfamily
B [auth C]IPR036419Ribosomal protein S3, C-terminal domain superfamilyHomologous Superfamily
B [auth C]IPR005704Small ribosomal subunit protein uS3, bacterial-typeFamily
B [auth C]IPR018280Small ribosomal subunit protein uS3, conserved siteConserved Site
T [auth Z]IPR004881Ribosome biogenesis GTPase RsgAFamily
T [auth Z]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
T [auth Z]IPR030378Circularly permuted (CP)-type guanine nucleotide-binding (G) domainDomain
T [auth Z]IPR010914RsgA GTPase domainDomain
T [auth Z]IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
D [auth E]IPR000851Small ribosomal subunit protein uS5Family
D [auth E]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
D [auth E]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
D [auth E]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
D [auth E]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
D [auth E]IPR005712Small ribosomal subunit protein uS5, bacterial-typeFamily
D [auth E]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
E [auth F]IPR020815Small ribosomal subunit protein bS6, conserved siteConserved Site
E [auth F]IPR000529Small ribosomal subunit protein bS6Family
E [auth F]IPR020814Small ribosomal subunit protein bS6, plastid/chloroplastFamily
E [auth F]IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
E [auth F]IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
F [auth G]IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
F [auth G]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
F [auth G]IPR000235Small ribosomal subunit protein uS7Family
F [auth G]IPR005717Small ribosomal subunit protein uS7, bacterial/organellar-typeFamily
F [auth G]IPR023798Small ribosomal subunit protein uS7 domainDomain
G [auth H]IPR000630Small ribosomal subunit protein uS8Family
G [auth H]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
G [auth H]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
H [auth I]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
H [auth I]IPR023035Small ribosomal subunit protein uS9, bacterial/plastidFamily
H [auth I]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
H [auth I]IPR000754Small ribosomal subunit protein uS9Family
H [auth I]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
I [auth J]IPR027486Small ribosomal subunit protein uS10 domainDomain
I [auth J]IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
I [auth J]IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site
I [auth J]IPR001848Small ribosomal subunit protein uS10Family