6YBW | pdb_00006ybw

Structure of a human 48S translational initiation complex - 40S body


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth J]SCOP2B SuperfamilyRibosomal protein S8 8095469 3000709 SCOP2B (2022-06-29)
H [auth K]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8053139 3000068 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyRibosomal protein S30e-like 8053453 3002190 SCOP2B (2022-06-29)
U [auth I]SCOP2B SuperfamilyHomeodomain-like 8052958 3000001 SCOP2B (2022-06-29)
U [auth I]SCOP2B SuperfamilyS15/NS1 RNA-binding domain 8052959 3001284 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyRibosomal S17 N-terminal domain-like 8052715 3002138 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyNucleic acid-binding proteins 8052717 3000135 SCOP2B (2022-06-29)
Q [auth R]SCOP2B Superfamily50S Ribosomal protein L14-like 8053077 3000433 SCOP2B (2022-06-29)
P [auth S]SCOP2B SuperfamilyGS N-terminal domain-like 8053171 3000408 SCOP2B (2022-06-29)
O [auth P]SCOP2B SuperfamilyTranslational machinery components 8098844 3000571 SCOP2B (2022-06-29)
N [auth Q]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8053143 3000068 SCOP2B (2022-06-29)
M [auth N]SCOP2B SuperfamilySIS domain/Ribosomal protein S2-like 8052791 3001397 SCOP2B (2022-06-29)
L [auth O]SCOP2B SuperfamilyRibosomal S3Ae-like 8053212 3002166 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyTranslation proteins SH3-like KOW motif containing domain 8052757 3000334 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyNucleic acid-binding proteins 8052756 3000135 SCOP2B (2022-06-29)
A [auth C]SCOP2B SuperfamilyAlpha-L RNA-binding motif 8052755 3001473 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
I [auth J]Ribosomal_S8_N_1e6ybwJ1 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)
I [auth J]Ribosomal_S8_C_1e6ybwJ2 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 K]Ribosomal_S21ee6ybwK1 A: a+b two layersX: 40S ribosomal protein rpS21 (S21e) (From Topology)H: 40S ribosomal protein rpS21 (S21e) (From Topology)T: 40S ribosomal protein rpS21 (S21e)F: Ribosomal_S21eECOD (1.6)
G [auth H]Ribosomal_S27ee6ybwH1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_S27eECOD (1.6)
FRibosomal_S30e6ybwF1 A: extended segmentsX: 40S ribosomal protein S30 (S30e) (From Topology)H: 40S ribosomal protein S30 (S30e) (From Topology)T: 40S ribosomal protein S30 (S30e)F: Ribosomal_S30ECOD (1.6)
E [auth G]Ribosomal_S7e_Ne6ybwG1 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: 40S ribosomal protein S7-A (From Topology)T: 40S ribosomal protein S7-AF: Ribosomal_S7e_NECOD (1.6)
E [auth G]Ribosomal_S7e_C_1e6ybwG2 A: a+b two layersX: Alpha-lytic protease prodomain-likeH: 40S ribosomal protein S7-A (From Topology)T: 40S ribosomal protein S7-AF: Ribosomal_S7e_C_1ECOD (1.6)
DS4e6ybwD1 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: S4ECOD (1.6)
C [auth E]Ribosom_S12_S23e6ybwE1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosom_S12_S23ECOD (1.6)
X [auth 9]Ribosomal_L41e6ybw91 A: extended segmentsX: Ribosomal protein L41-A (From Topology)H: Ribosomal protein L41-A (From Topology)T: Ribosomal protein L41-AF: Ribosomal_L41ECOD (1.6)
U [auth I]Ribosomal_S13_Ne6ybwI2 A: alpha arraysX: HTHH: 40S ribosomal protein S13 N-terminal domain (From Topology)T: 40S ribosomal protein S13 N-terminal domainF: Ribosomal_S13_NECOD (1.6)
U [auth I]Ribosomal_S15_2e6ybwI1 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)
T [auth p]SUI1e6ybwp1 A: a+b two layersX: Glucose permease domain IIB-likeH: eIF1-like (From Topology)T: eIF1-likeF: SUI1ECOD (1.6)
BRibosomal_S17_1e6ybwB1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_S17_1ECOD (1.6)
S [auth q]eIF-1ae6ybwq1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: eIF-1aECOD (1.6)
R [auth T]Ribosomal_S24ee6ybwT1 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)
Q [auth R]Ribosomal_S8ee6ybwR1 A: beta barrelsX: Ribosomal protein L14-likeH: Ribosomal protein L14-related (From Topology)T: Ribosomal protein L14-relatedF: Ribosomal_S8eECOD (1.6)
P [auth S]Ribosomal_S6ee6ybwS1 A: beta barrelsX: Ribosomal protein L25-likeH: Ribosomal protein L25-like (From Topology)T: Ribosomal protein L25-likeF: Ribosomal_S6eECOD (1.6)
O [auth P]Ribosomal_S11e6ybwP1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_S11ECOD (1.6)
N [auth Q]Ribosomal_S26ee6ybwQ1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: Ribosomal_S26eECOD (1.6)
M [auth N]Ribosomal_S2_2e6ybwN1 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)
L [auth O]Ribosomal_S3Ae_Ne6ybwO1 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)
L [auth O]Ribosomal_S3Ae_Ce6ybwO2 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)
K [auth L]Ribosomal_S5_C_1e6ybwL3 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_C_1ECOD (1.6)
K [auth L]Ribosomal_S5_3e6ybwL2 A: a+b two layersX: dsRBD-likeH: dsRNA-binding domain-like (From Topology)T: dsRNA-binding domain-likeF: Ribosomal_S5_3ECOD (1.6)
K [auth L]Ribosomal_S5_2e6ybwL1 A: extended segmentsX: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)H: N-terminal region in 40S ribosomal protein rpS2 (S5p) (From Topology)T: N-terminal region in 40S ribosomal protein rpS2 (S5p)F: Ribosomal_S5_2ECOD (1.6)
A [auth C]Ribosomal_S4ee6ybwC1 A: beta barrelsX: OB-foldH: Nucleic acid-binding proteins (From Topology)T: Nucleic acid-binding proteinsF: Ribosomal_S4eECOD (1.6)
A [auth C]40S_S4_Ce6ybwC2 A: beta barrelsX: SH3H: SH3T: SH3F: 40S_S4_CECOD (1.6)
A [auth C]RS4NTe6ybwC3 A: a+b two layersX: beta-GraspH: Ubiquitin-relatedT: Alpha-L RNA-binding motifF: RS4NTECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
I [auth J]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8Domain
H [auth K]PF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
G [auth H]PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
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
C [auth E]PF00164Ribosomal protein S12/S23 (Ribosom_S12_S23)Ribosomal protein S12/S23This protein is known as S12 in bacteria and archaea and S23 in eukaryotes. Domain
X [auth 9]PF05162Ribosomal protein L41 (Ribosomal_L41)Ribosomal protein L41- Family
U [auth I]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17Domain
PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
R [auth T]PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
Q [auth R]PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
P [auth S]PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
O [auth P]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
N [auth Q]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
M [auth N]PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
M [auth N]PF1612240S ribosomal protein SA C-terminus (40S_SA_C)40S ribosomal protein SA C-terminus- Family
K [auth L]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domainDomain
K [auth L]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domainDomain
A [auth C]PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
A [auth C]PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
A [auth C]PF08071RS4NT (NUC023) domain (RS4NT)RS4NT (NUC023) domainThis is the N-terminal domain of Ribosomal S4 / S4e proteins. This domain is associated with S4 and KOW domains [1]. Domain
A [auth C]PF00467KOW motif (KOW)KOW motif- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
I [auth J]40S ribosomal protein S15a
H [auth K]40S ribosomal protein S21
G [auth H]40S ribosomal protein S27
40S ribosomal protein S30
E [auth G]40S ribosomal protein S7
40S ribosomal protein S9
C [auth E]40S ribosomal protein S23
Z [auth 7]mRNA---
Y [auth A]18S rRNA---
X [auth 9]60S ribosomal protein L41
W [auth y]Eukaryotic translation initiation factor 3 subunit C
V [auth z]Eukaryotic translation initiation factor 3 subunit J
U [auth I]40S ribosomal protein S13
T [auth p]Eukaryotic translation initiation factor 1
40S ribosomal protein S11
S [auth q]Eukaryotic translation initiation factor 1A, X-chromosomal
R [auth T]40S ribosomal protein S24
Q [auth R]40S ribosomal protein S8
P [auth S]40S ribosomal protein S6
O [auth P]40S ribosomal protein S14
N [auth Q]40S ribosomal protein S26
M [auth N]40S ribosomal protein SA
L [auth O]40S ribosomal protein S3a
K [auth L]40S ribosomal protein S2
J [auth M]40S ribosomal protein S17
A [auth C]40S ribosomal protein S4, X isoform

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
I [auth J]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
I [auth J]IPR000630Small ribosomal subunit protein uS8Family
I [auth J]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
H [auth K]IPR038579Small ribosomal subunit protein eS21 superfamilyHomologous Superfamily
H [auth K]IPR018279Small ribosomal subunit protein eS21, conserved siteConserved Site
H [auth K]IPR001931Small ribosomal subunit protein eS21Family
G [auth H]IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
G [auth H]IPR000592Small ribosomal subunit protein eS27Family
G [auth H]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
IPR019954Ubiquitin conserved siteConserved Site
IPR006846Small ribosomal subunit protein eS30Family
IPR039415Ubiquitin-like protein FUBIDomain
IPR000626Ubiquitin-like domainDomain
IPR019956Ubiquitin domainDomain
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
E [auth G]IPR000554Small ribosomal subunit protein eS7Family
E [auth G]IPR047861Small ribosomal subunit protein eS7, conserved siteConserved Site
IPR005710Small ribosomal subunit protein uS4, eukaryota/archaeaFamily
IPR002942RNA-binding S4 domainDomain
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
C [auth E]IPR006032Small ribosomal subunit protein uS12Family
C [auth E]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
C [auth E]IPR005680Small ribosomal subunit protein uS12, eukaryota/archaeaFamily
X [auth 9]IPR007836Large ribosomal subunit protein eS32Family
W [auth y]IPR008905Eukaryotic translation initiation factor 3 subunit C, N-terminal domainDomain
W [auth y]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
W [auth y]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
W [auth y]IPR027516Eukaryotic translation initiation factor 3 subunit CFamily
W [auth y]IPR000717Proteasome component (PCI) domainDomain
V [auth z]IPR013906Eukaryotic translation initiation factor 3 subunit JFamily
V [auth z]IPR023194Eukaryotic translation initiation factor 3-like domain superfamilyHomologous Superfamily
U [auth I]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
U [auth I]IPR000589Small ribosomal subunit protein uS15Family
U [auth I]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
U [auth I]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotaFamily
T [auth p]IPR005874Eukaryotic translation initiation factor SUI1Family
T [auth p]IPR001950SUI1 domainDomain
T [auth p]IPR036877SUI1 domain superfamilyHomologous Superfamily
IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
IPR032440Small ribosomal subunit protein uS17, N-terminalDomain
IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
IPR000266Small ribosomal subunit protein uS17Family
IPR028333Small ribosomal subunit protein uS17, archaeal/eukaryoticFamily
S [auth q]IPR018104Translation initiation factor 1A (eIF-1A), conserved siteConserved Site
S [auth q]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
S [auth q]IPR006196RNA-binding domain, S1, IF1 typeDomain
S [auth q]IPR001253Translation initiation factor 1A (eIF-1A)Family
R [auth T]IPR053709Eukaryotic Ribosomal Protein eS24Homologous Superfamily
R [auth T]IPR001976Small ribosomal subunit protein eS24Family
R [auth T]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
R [auth T]IPR018098Small ribosomal subunit protein eS24 conserved siteConserved Site
Q [auth R]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
Q [auth R]IPR018283Small ribosomal subunit protein eS8, conserved siteConserved Site
Q [auth R]IPR001047Small ribosomal subunit protein eS8Family
Q [auth R]IPR042563Small ribosomal subunit protein eS8 subdomain, eukaryotaHomologous Superfamily
P [auth S]IPR018282Small ribosomal subunit protein eS6, conserved siteConserved Site
P [auth S]IPR001377Small ribosomal subunit protein eS6Family
P [auth S]IPR014401Small ribosomal subunit protein eS6-likeFamily
O [auth P]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
O [auth P]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
O [auth P]IPR001971Small ribosomal subunit protein uS11Family
N [auth Q]IPR047864Ribosomal protein eS26, conserved siteConserved Site
N [auth Q]IPR038551Ribosomal protein eS26 superfamilyHomologous Superfamily
N [auth Q]IPR000892Small ribosomal subunit protein eS26Family
M [auth N]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
M [auth N]IPR001865Small ribosomal subunit protein uS2Family
M [auth N]IPR032281Small ribosomal subunit protein uS2, C-terminal domainDomain
M [auth N]IPR027498Small ribosomal subunit protein uS2, eukaryotaFamily
M [auth N]IPR027504Small ribosomal subunit protein uS2, vertebratesFamily
M [auth N]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
M [auth N]IPR005707Small ribosomal subunit protein uS2, eukaryota/archaeaFamily
L [auth O]IPR001593Small ribosomal subunit protein eS1Family
L [auth O]IPR027500Small ribosomal subunit protein eS1, eukaryotaFamily
L [auth O]IPR018281Small ribosomal subunit protein eS1, conserved siteConserved Site
K [auth L]IPR005711Small ribosomal subunit protein uS5, eukaryota_archaeaFamily
K [auth L]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
K [auth L]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
K [auth L]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
K [auth L]IPR000851Small ribosomal subunit protein uS5Family
K [auth L]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
K [auth L]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
J [auth M]IPR001210Small ribosomal subunit protein eS17Family
J [auth M]IPR036401Small ribosomal subunit protein eS17 superfamilyHomologous Superfamily
J [auth M]IPR018273Small ribosomal subunit protein eS17, conserved siteConserved Site
A [auth C]IPR013843Small ribosomal subunit protein eS4, N-terminalDomain
A [auth C]IPR032277Small ribosomal subunit protein eS4, C-terminal domainDomain
A [auth C]IPR013845Small ribosomal subunit protein eS4, central regionDomain
A [auth C]IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
A [auth C]IPR041982Small ribosomal subunit protein eS4, KOW domainDomain
A [auth C]IPR018199Small ribosomal subunit protein eS4, N-terminal, conserved siteConserved Site
A [auth C]IPR002942RNA-binding S4 domainDomain
A [auth C]IPR000876Small ribosomal subunit protein eS4Family
A [auth C]IPR038237Small ribosomal subunit protein eS4, central domain superfamilyHomologous Superfamily
A [auth C]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
A [auth C]IPR005824KOWDomain

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
I [auth J]PharosP62244
H [auth K]PharosP63220
G [auth H]PharosP42677
PharosP62861
E [auth G]PharosP62081
PharosP46781
C [auth E]PharosP62266
X [auth 9]PharosP62945
W [auth y]PharosQ99613
V [auth z]PharosO75822
U [auth I]PharosP62277
T [auth p]PharosP41567
PharosP62280
S [auth q]PharosP47813
R [auth T]PharosP62847
Q [auth R]PharosP62241
P [auth S]PharosP62753
O [auth P]PharosP62263
N [auth Q]PharosP62854
M [auth N]PharosP08865
K [auth L]PharosP15880
J [auth M]PharosP08708
A [auth C]PharosP62701