5ME0

Structure of the 30S Pre-Initiation Complex 1 (30S IC-1) Stalled by GE81112


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
BSCOP2B SuperfamilySIS domain/Ribosomal protein S2-like8063838 3001397 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRibosomal protein S68066495 3001323 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyRibosomal protein S78077979 3000799 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyRibosomal protein S88079059 3000709 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyRibosomal protein S5 domain 2-like8082661 3000100 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyRibosomal protein S108102681 3001336 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyTranslational machinery components8035368 3000571 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyNucleic acid-binding proteins8106545 3000135 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyS13-like H2TH domain8098358 3000053 SCOP2B (2022-06-29)
OSCOP2B SuperfamilyS15/NS1 RNA-binding domain8032375 3001284 SCOP2B (2022-06-29)
QSCOP2B SuperfamilyNucleic acid-binding proteins8059276 3000135 SCOP2B (2022-06-29)
SSCOP2B SuperfamilyRibosomal protein S198103915 3000686 SCOP2B (2022-06-29)
USCOP2B SuperfamilyRibosomal protein S218053090 3002159 SCOP2B (2022-06-29)
VSCOP2B SuperfamilyNucleic acid-binding proteins8041946 3000135 SCOP2B (2022-06-29)
X [auth Y]SCOP2B SuperfamilyTranslation initiation factor IF3 N-terminal domain8034611 3000407 SCOP2B (2022-06-29)
NSCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain)8052568 3000068 SCOP2B (2022-06-29)
Y [auth Z]SCOP2B SuperfamilyTranslation initiation factor IF3 C-terminal domain8035754 3001514 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyAlpha-L RNA-binding motif8083400 3001473 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
BRibosomal_S2e5me0B1 A: a/b three-layered sandwichesX: Flavodoxin-likeH: Ribosomal protein S2/SIS domain (From Topology)T: Ribosomal protein S2/SIS domainF: Ribosomal_S2ECOD (1.6)
CRibosomal_S3_Ce5me0C2 A: a+b two layersX: T-foldH: Ribosomal protein S3-C (From Topology)T: Ribosomal protein S3-CF: Ribosomal_S3_CECOD (1.6)
CKH_2_1e5me0C1 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)
ERibosomal_S5_Ce5me0E1 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)
ERibosomal_S5e5me0E2 A: a+b two layersX: dsRBD-likeH: dsRNA-binding domain-like (From Topology)T: dsRNA-binding domain-likeF: Ribosomal_S5ECOD (1.6)
FRibosomal_S6e5me0F1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S6 (From Topology)T: Ribosomal protein S6F: Ribosomal_S6ECOD (1.6)
GRibosomal_S7_1e5me0G1 A: alpha arraysX: Ribosomal protein S7 (From Topology)H: Ribosomal protein S7 (From Topology)T: Ribosomal protein S7F: Ribosomal_S7_1ECOD (1.6)
HRibosomal_S8_Ne5me0H1 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)
HRibosomal_S8_Ce5me0H2 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)
IRibosomal_S9e5me0I1 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)
JRibosomal_S10e5me0J1 A: a+b two layersX: Alpha-beta plaitsH: Ribosomal protein S10 (From Topology)T: Ribosomal protein S10F: Ribosomal_S10ECOD (1.6)
KRibosomal_S11e5me0K1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_S11ECOD (1.6)
LRibosom_S12_S23e5me0L1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosom_S12_S23ECOD (1.6)
MRibosomal_S13_1e5me0M1 A: alpha arraysX: HhH/H2THH: H2TH (From Topology)T: H2THF: Ribosomal_S13_1ECOD (1.6)
ORibosomal_S15_1e5me0O1 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)
PRibosomal_S16e5me0P1 A: a+b two layersX: Ribosomal protein S16 (From Topology)H: Ribosomal protein S16 (From Topology)T: Ribosomal protein S16F: Ribosomal_S16ECOD (1.6)
QRibosomal_S17_1e5me0Q1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_S17_1ECOD (1.6)
SRibosomal_S19e5me0S1 A: a+b two layersX: Ribosomal protein S19 (From Topology)H: Ribosomal protein S19 (From Topology)T: Ribosomal protein S19F: Ribosomal_S19ECOD (1.6)
TRibosomal_S20pe5me0T1 A: alpha bundlesX: Spectrin repeat-likeH: Ribosomal protein S20 (From Topology)T: Ribosomal protein S20F: Ribosomal_S20pECOD (1.6)
URibosomal_S21e5me0U1 A: extended segmentsX: 30S ribosomal protein S21 (From Topology)H: 30S ribosomal protein S21 (From Topology)T: 30S ribosomal protein S21F: Ribosomal_S21ECOD (1.6)
VeIF-1ae5me0V1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: eIF-1aECOD (1.6)
WGTP_EFTU_D2_3e5me0W2 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: GTP_EFTU_D2_3ECOD (1.6)
WGTP_EFTU_D2e5me0W1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: Alanine racemase-CF: GTP_EFTU_D2ECOD (1.6)
WMnmE_helical_2nde5me0W3 A: a/b three-layered sandwichesX: P-loop domains-likeH: P-loop domains-relatedT: P-loop containing nucleoside triphosphate hydrolasesF: MnmE_helical_2ndECOD (1.6)
WIF-2e5me0W4 A: a/b three-layered sandwichesX: Initiation factor IF2/eIF5b, domain 3 (From Topology)H: Initiation factor IF2/eIF5b, domain 3 (From Topology)T: Initiation factor IF2/eIF5b, domain 3F: IF-2ECOD (1.6)
X [auth Y]IF3_Ne5me0Y1 A: a+b two layersX: beta-GraspH: IF3-N (From Topology)T: IF3-NF: IF3_NECOD (1.6)
NRibosomal_S14_1e5me0N1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: Ribosomal_S14_1ECOD (1.6)
RRibosomal_S18e5me0R1 A: alpha arraysX: HTHH: HTHT: tri-helicalF: Ribosomal_S18ECOD (1.6)
Y [auth Z]IF3_Ce5me0Z1 A: a+b two layersX: IF3-likeH: Translation initiation factor IF3, C-terminal domain (From Topology)T: Translation initiation factor IF3, C-terminal domainF: IF3_CECOD (1.6)
DS4e5me0D1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: S4ECOD (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
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
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
PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes.Domain
PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23- Family
PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15- Domain
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17- Domain
PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19- Domain
PF01649Ribosomal protein S20 (Ribosomal_S20p)Ribosomal protein S20- Family
PF01165Ribosomal protein S21 (Ribosomal_S21)Ribosomal protein S21- 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
PF11987Translation-initiation factor 2 (IF-2)Translation-initiation factor 2IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 pr ...IF-2 is a translation initiator in each of the three main phylogenetic domains (Eukaryotes [1], Bacteria [2] and Archaea [3]). IF2 interacts with formylmethionine-tRNA, GTP, IF1, IF3 and both ribosomal subunits [2]. Through these interactions, IF2 promotes the binding of the initiator tRNA to the A site in the smaller ribosomal subunit and catalyses the hydrolysis of GTP following initiation-complex formation [2].
Domain
X [auth Y]PF05198Translation initiation factor IF-3, N-terminal domain (IF3_N)Translation initiation factor IF-3, N-terminal domain- Domain
PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
PF01084Ribosomal protein S18 (Ribosomal_S18)Ribosomal protein S18- Family
Y [auth Z]PF00707Translation initiation factor IF-3, C-terminal domain (IF3_C)Translation initiation factor IF-3, C-terminal domain- 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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
16S ribosomal RNA---
30S ribosomal protein S2
30S ribosomal protein S3
30S ribosomal protein S5
30S ribosomal protein S6
30S ribosomal protein S7
30S ribosomal protein S8
30S ribosomal protein S9
30S ribosomal protein S10
30S ribosomal protein S11
30S ribosomal protein S12
30S ribosomal protein S13
30S ribosomal protein S15
30S ribosomal protein S16---
30S ribosomal protein S17
30S ribosomal protein S19
30S ribosomal protein S20
30S ribosomal protein S21
Translation initiation factor IF-1 -
Translation initiation factor IF-2
X [auth Y]Translation initiation factor IF-3 -
Z [auth X]fMet-tRNA---
30S ribosomal protein S14
30S ribosomal protein S18
Y [auth Z]Translation initiation factor IF-3
30S ribosomal protein S4

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
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
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
IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
IPR000235Small ribosomal subunit protein uS7Family
IPR005717Small ribosomal subunit protein uS7, bacterial/organellar-typeFamily
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
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
IPR027486Small ribosomal subunit protein uS10 domainDomain
IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site
IPR001848Small ribosomal subunit protein uS10Family
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
IPR005679Ribosomal protein uS12, bacterial-typeFamily
IPR006032Small ribosomal subunit protein uS12Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
IPR001892Small ribosomal subunit protein uS13Family
IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
IPR019980Small ribosomal subunit protein uS13, bacterial-typeFamily
IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
IPR000589Small ribosomal subunit protein uS15Family
IPR005290Small ribosomal subunit protein uS15, bacterial-typeFamily
IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
IPR019984Small ribosomal subunit protein uS17, bacteria/chloroplastFamily
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR000266Small ribosomal subunit protein uS17Family
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
IPR036510Small ribosomal subunit protein bS20 superfamilyHomologous Superfamily
IPR002583Small ribosomal subunit protein bS20Family
IPR038380Small ribosomal subunit protein bS21 superfamilyHomologous Superfamily
IPR018278Small ribosomal subunit protein bS21, conserved siteConserved Site
IPR001911Small ribosomal subunit protein bS21Family
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR006196RNA-binding domain, S1, IF1 typeDomain
IPR004368Translation initiation factor IF-1Family
IPR009061Putative DNA-binding domain superfamilyHomologous Superfamily
IPR000178Translation initiation factor IF-2, bacterial-likeFamily
IPR000795Translational (tr)-type GTP-binding domainDomain
IPR013575Initiation factor 2 associated domain, bacterialDomain
IPR004161Translation elongation factor EFTu-like, domain 2Domain
IPR006847Translation initiation factor IF-2, N-terminalDomain
IPR044145Translation initiation factor IF-2, domain IIDomain
IPR009000Translation protein, beta-barrel domain superfamilyHomologous Superfamily
IPR005225Small GTP-binding protein domainDomain
IPR015760Translation initiation factor IF- 2Family
IPR036925Translation initiation factor IF-2, domain 3 superfamilyHomologous Superfamily
IPR023115Translation initiation factor IF- 2, domain 3Domain
IPR027417P-loop containing nucleoside triphosphate hydrolaseHomologous Superfamily
X [auth Y]IPR019815Translation initiation factor 3, C-terminalDomain
X [auth Y]IPR036787Translation initiation factor 3 (IF-3), N-terminal domain superfamilyHomologous Superfamily
X [auth Y]IPR001288Translation initiation factor 3Family
X [auth Y]IPR019814Translation initiation factor 3, N-terminalDomain
X [auth Y]IPR019813Translation initiation factor 3, conserved siteConserved Site
X [auth Y]IPR036788Translation initiation factor 3 (IF-3), C-terminal domain superfamilyHomologous Superfamily
IPR001209Small ribosomal subunit protein uS14Family
IPR018271Small ribosomal subunit protein uS14, conserved siteConserved Site
IPR023036Small ribosomal subunit protein uS14, bacteria/plastidFamily
IPR001648Small ribosomal subunit protein bS18Family
IPR018275Small ribosomal subunit protein bS18, conserved siteConserved Site
IPR036870Small ribosomal subunit protein bS18 superfamilyHomologous Superfamily
Y [auth Z]IPR019815Translation initiation factor 3, C-terminalDomain
Y [auth Z]IPR001288Translation initiation factor 3Family
Y [auth Z]IPR019814Translation initiation factor 3, N-terminalDomain
Y [auth Z]IPR036788Translation initiation factor 3 (IF-3), C-terminal domain superfamilyHomologous Superfamily
Y [auth Z]IPR036787Translation initiation factor 3 (IF-3), N-terminal domain superfamilyHomologous Superfamily
Y [auth Z]IPR019813Translation initiation factor 3, conserved siteConserved Site
IPR002942RNA-binding S4 domainDomain
IPR005709Small ribosomal subunit protein uS4, bacterial-typeFamily
IPR022801Small ribosomal subunit protein uS4Family
IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily