1I97

CRYSTAL STRUCTURE OF THE 30S RIBOSOMAL SUBUNIT FROM THERMUS THERMOPHILUS IN COMPLEX WITH TETRACYCLINE


Domain Annotation: SCOP/SCOPe Classification SCOP Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Bd1i97b_ Alpha and beta proteins (a/b) Flavodoxin-like Ribosomal protein S2 Ribosomal protein S2 Ribosomal protein S2 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Cd1i97c1 Alpha and beta proteins (a+b) Alpha-lytic protease prodomain-like Prokaryotic type KH domain (KH-domain type II) Prokaryotic type KH domain (KH-domain type II) Ribosomal protein S3 N-terminal domain (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Cd1i97c2 Alpha and beta proteins (a+b) Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Fd1i97f_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S6 Ribosomal protein S6 Ribosomal protein S6 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Gd1i97g_ All alpha proteins Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Hd1i97h_ Alpha and beta proteins (a+b) Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Jd1i97j_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S10 Ribosomal protein S10 Ribosomal protein S10 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ld1i97l_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S12 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Md1i97m_ All alpha proteins S13-like H2TH domain S13-like H2TH domain Ribosomal protein S13 Ribosomal protein S13 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Nd1i97n_ Small proteins Glucocorticoid receptor-like (DNA-binding domain) Glucocorticoid receptor-like (DNA-binding domain) Ribosomal protein S14 Ribosomal protein S14 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Qd1i97q_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S17 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Rd1i97r_ All alpha proteins DNA/RNA-binding 3-helical bundle Ribosomal protein S18 Ribosomal protein S18 Ribosomal protein S18 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Td1i97t_ All alpha proteins Spectrin repeat-like Ribosomal protein S20 Ribosomal protein S20 Ribosomal protein S20 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ud1i97u_ Peptides Arg-rich RNA binding peptides 30S ribosomal protein THX 30S ribosomal protein THX 30S ribosomal protein THX (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Kd1i97k_ Alpha and beta proteins (a/b) Ribonuclease H-like motif Translational machinery components Ribosomal protein L18 and S11 Ribosomal protein S11 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Od1i97o_ All alpha proteins S15/NS1 RNA-binding domain S15/NS1 RNA-binding domain Ribosomal protein S15 Ribosomal protein S15 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Pd1i97p_ Alpha and beta proteins (a+b) Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Sd1i97s_ Alpha and beta proteins (a+b) Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Dd1i97d_ Alpha and beta proteins (a+b) Alpha-L RNA-binding motif Alpha-L RNA-binding motif Ribosomal protein S4 (bacteria) Ribosomal protein S4 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ed1i97e1 Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S5, C-terminal domain (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Ed1i97e2 Alpha and beta proteins (a+b) dsRBD-like dsRNA-binding domain-like Ribosomal S5 protein, N-terminal domain Ribosomal S5 protein, N-terminal domain (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)
Id1i97i_ Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S9 (Thermus thermophilus ) [TaxId: 274 ], SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilySIS domain/Ribosomal protein S2-like8044010 3001397 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyRibosomal protein S3 C-terminal domain8044012 3001053 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyProkaryotic type KH domain (KH-domain type II)8044011 3001043 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRibosomal protein S78033523 3000799 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRibosomal protein S108044019 3001336 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyNucleic acid-binding proteins8044021 3000135 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyS13-like H2TH domain8003708 3000053 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain)8052585 3000068 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyNucleic acid-binding proteins8044026 3000135 SCOP2B (2022-06-29)
RSCOP2B SuperfamilyRibosomal protein S188044028 3001191 SCOP2B (2022-06-29)
TSCOP2B SuperfamilyRibosomal protein S208044029 3001362 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyTranslational machinery components8044020 3000571 SCOP2B (2022-06-29)
PSCOP2B SuperfamilyRibosomal protein S168044025 3000680 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyRibosomal protein S198044027 3000686 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyAlpha-L RNA-binding motif8044014 3001473 SCOP2B (2022-06-29)
ESCOP2B SuperfamilydsRNA-binding domain-like8044017 3000985 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyRibosomal protein S5 domain 2-like8044015 3000100 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRibosomal protein S5 domain 2-like8037678 3000100 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BPF00318e1i97B1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Ribosomal protein S2/SIS domain (From Topology)T: Ribosomal protein S2/SIS domainF: PF00318ECOD (1.6)
CPF00189e1i97C1 A: a+b two layersX: T-foldH: Ribosomal protein S3-C (From Topology)T: Ribosomal protein S3-CF: PF00189ECOD (1.6)
CPF07650e1i97C2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: KH-domainsT: Prokaryotic type KH domain (KH-domain type II)F: PF07650ECOD (1.6)
FPF01250e1i97F1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S6 (From Topology)T: Ribosomal protein S6F: PF01250ECOD (1.6)
GPF00177e1i97G1 A: alpha arraysX: Ribosomal protein S7 (From Topology)H: Ribosomal protein S7 (From Topology)T: Ribosomal protein S7F: PF00177ECOD (1.6)
HPF00410e1i97H1 A: a+b two layersX: R3H domain-likeH: Ribosomal protein S8, N-terminal domain (From Topology)T: Ribosomal protein S8, N-terminal domainF: PF00410ECOD (1.6)
HPF00410e1i97H2 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: PF00410ECOD (1.6)
JPF00338e1i97J1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S10 (From Topology)T: Ribosomal protein S10F: PF00338ECOD (1.6)
LPF00164e1i97L1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00164ECOD (1.6)
MPF00416e1i97M1 A: alpha arraysX: HhH/H2THH: H2TH (From Topology)T: H2THF: PF00416ECOD (1.6)
NPF00253e1i97N1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: PF00253ECOD (1.6)
QPF00366e1i97Q1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: PF00366ECOD (1.6)
RPF01084e1i97R1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: PF01084ECOD (1.6)
TPF01649e1i97T1 A: alpha bundlesX: Spectrin repeat-likeH: Ribosomal protein S20 (From Topology)T: Ribosomal protein S20F: PF01649ECOD (1.6)
KPF00411e1i97K1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: PF00411ECOD (1.6)
OPF00312e1i97O1 A: alpha arraysX: S15/NS1 RNA-binding domain (From Topology)H: S15/NS1 RNA-binding domain (From Topology)T: S15/NS1 RNA-binding domainF: PF00312ECOD (1.6)
PPF00886e1i97P1 A: a+b two layersX: Ribosomal protein S16 (From Topology)H: Ribosomal protein S16 (From Topology)T: Ribosomal protein S16F: PF00886ECOD (1.6)
SPF00203e1i97S1 A: a+b two layersX: Ribosomal protein S19 (From Topology)H: Ribosomal protein S19 (From Topology)T: Ribosomal protein S19F: PF00203ECOD (1.6)
DPF00163,PF01479e1i97D1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: PF00163,PF01479ECOD (1.6)
EPF03719e1i97E2 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: PF03719ECOD (1.6)
EPF00333e1i97E1 A: a+b two layersX: dsRBD-likeH: dsRNA-binding domain-like (From Topology)T: dsRNA-binding domain-likeF: PF00333ECOD (1.6)
IPF00380e1i97I1 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: PF00380ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
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
PF01250Ribosomal protein S6 (Ribosomal_S6)Ribosomal protein S6- Domain
PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes.Domain
PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8- Domain
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
PF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
PF1707030S ribosomal protein Thx (Thx)30S ribosomal protein Thx- Family
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00886Ribosomal protein S16 (Ribosomal_S16)Ribosomal protein S16- Family
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- 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
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
16S RRNA---
30S RIBOSOMAL PROTEIN S2
30S RIBOSOMAL PROTEIN S3
30S RIBOSOMAL PROTEIN S6
30S RIBOSOMAL PROTEIN S7
30S RIBOSOMAL PROTEIN S8
30S RIBOSOMAL PROTEIN S10
30S RIBOSOMAL PROTEIN S12
30S RIBOSOMAL PROTEIN S13
30S RIBOSOMAL PROTEIN S14
30S RIBOSOMAL PROTEIN S17
30S RIBOSOMAL PROTEIN S18
30S RIBOSOMAL PROTEIN S20
30S RIBOSOMAL PROTEIN THX -
30S RIBOSOMAL PROTEIN S11
30S RIBOSOMAL PROTEIN S15
30S RIBOSOMAL PROTEIN S16
30S RIBOSOMAL PROTEIN S19
30S RIBOSOMAL PROTEIN S4
30S RIBOSOMAL PROTEIN S5
30S RIBOSOMAL PROTEIN S9

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR005706Small ribosomal subunit protein uS2, bacteria/mitochondria/plastidFamily
IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
IPR001865Small ribosomal subunit protein uS2Family
IPR001351Small ribosomal subunit protein uS3, C-terminalDomain
IPR009019K homology domain superfamily, prokaryotic typeHomologous Superfamily
IPR004087K Homology domainDomain
IPR004044K Homology domain, type 2Domain
IPR015946K homology domain-like, alpha/betaHomologous Superfamily
IPR036419Ribosomal protein S3, C-terminal domain superfamilyHomologous Superfamily
IPR005704Small ribosomal subunit protein uS3, bacterial-typeFamily
IPR018280Small ribosomal subunit protein uS3, conserved siteConserved Site
IPR020815Small ribosomal subunit protein bS6, conserved siteConserved Site
IPR000529Small ribosomal subunit protein bS6Family
IPR020814Small ribosomal subunit protein bS6, plastid/chloroplastFamily
IPR035980Small ribosomal subunit protein bS6 superfamilyHomologous Superfamily
IPR014717Translation elongation factor EF1B/small ribosomal subunit protein bS6Homologous Superfamily
IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
IPR000235Small ribosomal subunit protein uS7Family
IPR005717Small ribosomal subunit protein uS7, bacterial/organellar-typeFamily
IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
IPR023798Small ribosomal subunit protein uS7 domainDomain
IPR000630Small ribosomal subunit protein uS8Family
IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
IPR001848Small ribosomal subunit protein uS10Family
IPR027486Small ribosomal subunit protein uS10 domainDomain
IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site
IPR006032Small ribosomal subunit protein uS12Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR005679Ribosomal protein uS12, bacterial-typeFamily
IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
IPR001892Small ribosomal subunit protein uS13Family
IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
IPR019980Small ribosomal subunit protein uS13, bacterial-typeFamily
IPR023053Small ribosomal subunit protein uS14, bacteriaFamily
IPR001209Small ribosomal subunit protein uS14Family
IPR018271Small ribosomal subunit protein uS14, conserved siteConserved Site
IPR043140Small ribosomal subunit protein uS14 superfamilyHomologous Superfamily
IPR019984Small ribosomal subunit protein uS17, bacteria/chloroplastFamily
IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR000266Small ribosomal subunit protein uS17Family
IPR001648Small ribosomal subunit protein bS18Family
IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
IPR036510Small ribosomal subunit protein bS20 superfamilyHomologous Superfamily
IPR002583Small ribosomal subunit protein bS20Family
IPR030826Small ribosomal subunit protein bTHX/bTHXc/bTHXmFamily
IPR031414Small ribosomal subunit protein bTHXFamily
IPR001971Small ribosomal subunit protein uS11Family
IPR019981Small ribosomal subunit protein uS11, bacterial-typeFamily
IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
IPR000589Small ribosomal subunit protein uS15Family
IPR023803Small ribosomal subunit protein bS16 domain superfamilyHomologous Superfamily
IPR000307Small ribosomal subunit protein bS16Family
IPR002222Small ribosomal subunit protein uS19Family
IPR005732Small ribosomal subunit protein uS19, bacterial-typeFamily
IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
IPR002942RNA-binding S4 domainDomain
IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
IPR005709Small ribosomal subunit protein uS4, bacterial-typeFamily
IPR022801Small ribosomal subunit protein uS4Family
IPR000851Small ribosomal subunit protein uS5Family
IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
IPR005712Small ribosomal subunit protein uS5, bacterial-typeFamily
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
IPR023035Small ribosomal subunit protein uS9, bacterial/plastidFamily
IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
IPR000754Small ribosomal subunit protein uS9Family
IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily