8CDV

Rnase R bound to a 30S degradation intermediate (state II)


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
J [auth L]SCOP2B SuperfamilyNucleic acid-binding proteins 8098574 3000135 SCOP2B (2022-06-29)
K [auth M]SCOP2B SuperfamilyS13-like H2TH domain 8098564 3000053 SCOP2B (2022-06-29)
L [auth O]SCOP2B SuperfamilyS15/NS1 RNA-binding domain 8072617 3001284 SCOP2B (2022-06-29)
M [auth P]SCOP2B SuperfamilyRibosomal protein S16 8066553 3000680 SCOP2B (2022-06-29)
N [auth Q]SCOP2B SuperfamilyNucleic acid-binding proteins 8059270 3000135 SCOP2B (2022-06-29)
O [auth R]SCOP2B SuperfamilyRibosomal protein S19 8086056 3000686 SCOP2B (2022-06-29)
Q [auth T]SCOP2B SuperfamilyRibosomal protein S6 8066497 3001323 SCOP2B (2022-06-29)
D [auth F]SCOP2B SuperfamilyAlpha-L RNA-binding motif 8083390 3001473 SCOP2B (2022-06-29)
G [auth I]SCOP2B SuperfamilyRibosomal protein S8 8079051 3000709 SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
J [auth L]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
K [auth M]PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
L [auth O]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
M [auth P]PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
N [auth Q]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
Q [auth T]PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
R [auth U]PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
S [auth V]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00773RNB domain (RNB)RNB domainThis domain is the catalytic domain of ribonuclease II [1].Domain
D [auth F]PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
D [auth F]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
E [auth G]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domain- Domain
E [auth G]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domain- Domain
G [auth I]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
H [auth J]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
I [auth K]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 rRNA---
J [auth L]30S ribosomal protein S12
K [auth M]30S ribosomal protein S13
L [auth O]30S ribosomal protein S15
M [auth P]30S ribosomal protein S16
N [auth Q]30S ribosomal protein S17
O [auth R]30S ribosomal protein S19
P [auth S]30S ribosomal protein S20
Q [auth T]30S ribosomal protein S6
R [auth U]30S ribosomal protein S18
S [auth V]30S ribosomal protein S11
RNA Substrate---
Ribonuclease R
D [auth F]30S ribosomal protein S4
E [auth G]30S ribosomal protein S5
F [auth H]30S ribosomal protein S7
G [auth I]30S ribosomal protein S8
H [auth J]30S ribosomal protein S9
I [auth K]30S ribosomal protein S10

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
J [auth L]IPR006032Small ribosomal subunit protein uS12Family
J [auth L]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
J [auth L]IPR005679Ribosomal protein uS12, bacterial-typeFamily
K [auth M]IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
K [auth M]IPR001892Small ribosomal subunit protein uS13Family
K [auth M]IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
K [auth M]IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
K [auth M]IPR019980Small ribosomal subunit protein uS13, bacterial-typeFamily
L [auth O]IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
L [auth O]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
L [auth O]IPR000589Small ribosomal subunit protein uS15Family
M [auth P]IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
M [auth P]IPR000307Small ribosomal subunit protein bS16Family
M [auth P]IPR020592Small ribosomal subunit protein bS16, conserved siteConserved Site
N [auth Q]IPR019984Small ribosomal subunit protein uS17, bacteria/chloroplastFamily
N [auth Q]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
N [auth Q]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
N [auth Q]IPR000266Small ribosomal subunit protein uS17Family
O [auth R]IPR002222Small ribosomal subunit protein uS19Family
O [auth R]IPR005732Small ribosomal subunit protein uS19, bacterial-typeFamily
O [auth R]IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
O [auth R]IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
P [auth S]IPR036510Small ribosomal subunit protein bS20 superfamilyHomologous Superfamily
P [auth S]IPR002583Small ribosomal subunit protein bS20Family
Q [auth T]IPR020815Small ribosomal subunit protein bS6, conserved siteConserved Site
Q [auth T]IPR000529Small ribosomal subunit protein bS6Family
Q [auth T]IPR020814Small ribosomal subunit protein bS6, plastid/chloroplastFamily
Q [auth T]IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
Q [auth T]IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
R [auth U]IPR001648Small ribosomal subunit protein bS18Family
R [auth U]IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
R [auth U]IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
S [auth V]IPR001971Small ribosomal subunit protein uS11Family
S [auth V]IPR019981Small ribosomal subunit protein uS11, bacterial-typeFamily
S [auth V]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
S [auth V]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
IPR011129Cold-shock domainDomain
IPR003029S1 domainDomain
IPR013223Ribonuclease B, N-terminal OB domainDomain
IPR050180RNR RibonucleaseFamily
IPR040476RNase II/RNase R, cold shock domainDomain
IPR022966Ribonuclease II/R, conserved siteConserved Site
IPR004476Ribonuclease II/ribonuclease RFamily
IPR001900Ribonuclease II/RDomain
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR011805Ribonuclease RFamily
D [auth F]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
D [auth F]IPR002942RNA-binding S4 domainDomain
D [auth F]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
D [auth F]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
D [auth F]IPR005709Small ribosomal subunit protein uS4, bacterial-typeFamily
D [auth F]IPR022801Small ribosomal subunit protein uS4Family
E [auth G]IPR000851Small ribosomal subunit protein uS5Family
E [auth G]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
E [auth G]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
E [auth G]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
E [auth G]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
E [auth G]IPR005712Small ribosomal subunit protein uS5, bacterial-typeFamily
E [auth G]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
F [auth H]IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
F [auth H]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
F [auth H]IPR000235Small ribosomal subunit protein uS7Family
F [auth H]IPR005717Small ribosomal subunit protein uS7, bacterial/organellar-typeFamily
F [auth H]IPR023798Small ribosomal subunit protein uS7 domainDomain
G [auth I]IPR000630Small ribosomal subunit protein uS8Family
G [auth I]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
G [auth I]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
H [auth J]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
H [auth J]IPR023035Small ribosomal subunit protein uS9, bacterial/plastidFamily
H [auth J]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
H [auth J]IPR000754Small ribosomal subunit protein uS9Family
H [auth J]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
I [auth K]IPR001848Small ribosomal subunit protein uS10Family
I [auth K]IPR027486Small ribosomal subunit protein uS10 domainDomain
I [auth K]IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
I [auth K]IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site