6YBD | pdb_00006ybd

Structure of a human 48S translational initiation complex - eIF3


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
I [auth K]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8053139 3000068 SCOP2B (2022-06-29)
L [auth O]SCOP2B SuperfamilyRibosomal S3Ae-like 8053212 3002166 SCOP2B (2022-06-29)
M [auth N]SCOP2B SuperfamilySIS domain/Ribosomal protein S2-like 8052791 3001397 SCOP2B (2022-06-29)
O [auth P]SCOP2B SuperfamilyTranslational machinery components 8098844 3000571 SCOP2B (2022-06-29)
P [auth I]SCOP2B SuperfamilyHomeodomain-like 8052958 3000001 SCOP2B (2022-06-29)
P [auth I]SCOP2B SuperfamilyS15/NS1 RNA-binding domain 8052959 3001284 SCOP2B (2022-06-29)
F [auth 8]SCOP2B SuperfamilyJAB1/MPN domain-like 8053284 3001105 SCOP2B (2022-06-29)
E [auth y]SCOP2B SuperfamilyTPR-like 8093044 3001345 SCOP2B (2022-06-29)
E [auth y]SCOP2B SuperfamilyWinged helix DNA-binding domain 8093051 3000034 SCOP2B (2022-06-29)
D [auth v]SCOP2B SuperfamilyTPR-like 8091483 3001345 SCOP2B (2022-06-29)
D [auth v]SCOP2B SuperfamilyWinged helix DNA-binding domain 8091486 3000034 SCOP2B (2022-06-29)
B [auth 4]SCOP2B SuperfamilyJAB1/MPN domain-like 8053242 3001105 SCOP2B (2022-06-29)
B [auth 4]SCOP2B SuperfamilyEIF3 subunit F C-terminal domain-like 8053241 3002167 SCOP2B (2022-06-29)
R [auth 3]SCOP2B SuperfamilyARM repeat-like 8002866 3000116 SCOP2B (2022-06-29)
R [auth 3]SCOP2B SuperfamilyWinged helix DNA-binding domain 8002864 3000034 SCOP2B (2022-06-29)
N [auth Q]SCOP2B SuperfamilyGlucocorticoid receptor-like (DNA-binding domain) 8053143 3000068 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
GRibosomal_S7e_Ne6ybdG1 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)
GRibosomal_S7e_C_1e6ybdG2 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)
HRibosomal_S27ee6ybdH1 A: few secondary structure elementsX: Rubredoxin-likeH: Rubredoxin-relatedT: Rubredoxin-relatedF: Ribosomal_S27eECOD (1.6)
I [auth K]Ribosomal_S21ee6ybdK1 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)
K [auth L]Ribosomal_S5_C_1e6ybdL3 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_3e6ybdL2 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_2e6ybdL1 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)
L [auth O]Ribosomal_S3Ae_Ne6ybdO1 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_Ce6ybdO2 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)
M [auth N]Ribosomal_S2_2e6ybdN1 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)
O [auth P]Ribosomal_S11e6ybdP1 A: mixed a+b and a/bX: Ribonuclease H-likeH: Ribonuclease H-like (From Topology)T: Ribonuclease H-likeF: Ribosomal_S11ECOD (1.6)
P [auth I]Ribosomal_S13_Ne6ybdI1 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)
P [auth I]Ribosomal_S15_2e6ybdI2 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)
F [auth 8]JAB_1e6ybd81 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: JAB_1ECOD (1.6)
F [auth 8]KOG1560e6ybd82 A: extended segmentsX: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)H: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)T: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domainF: KOG1560ECOD (1.6)
E [auth y]PCIe6ybdy1 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
E [auth y]eIF-3c_Ne6ybdy2 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: eIF-3c_NECOD (1.6)
D [auth v]PCIe6ybdv3 A: alpha arraysX: HTHH: HTHT: wingedF: PCIECOD (1.6)
D [auth v]eIF3_Ne6ybdv1 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: eIF3_NECOD (1.6)
D [auth v]KOG2758e6ybdv2 A: extended segmentsX: 26S proteasome regulatory subunits C-terminal helicesH: 26S proteasome regulatory subunit RPN7 C-terminal helix (From Topology)T: 26S proteasome regulatory subunit RPN7 C-terminal helixF: KOG2758ECOD (1.6)
B [auth 4]JAB_1e6ybd41 A: a+b three layersX: Cytidine deaminase-like (From Topology)H: Cytidine deaminase-like (From Topology)T: Cytidine deaminase-likeF: JAB_1ECOD (1.6)
B [auth 4]MitMem_rege6ybd42 A: extended segmentsX: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)H: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domain (From Topology)T: 26S proteasome regulatory subunit RPN8/RPN11 C-terminal domainF: MitMem_regECOD (1.6)
R [auth 3]CSN8_PSD8_EIF3K_Ce6ybd32 A: alpha arraysX: HTHH: HTHT: wingedF: CSN8_PSD8_EIF3K_CECOD (1.6)
R [auth 3]SAC3_GANP_1ste6ybd31 A: alpha superhelicesX: Repetitive alpha hairpinsH: ARM repeat (From Topology)T: ARM repeatF: SAC3_GANP_1stECOD (1.6)
N [auth Q]Ribosomal_S26ee6ybdQ1 A: few secondary structure elementsX: Glucocorticoid receptor-likeH: LIM domain-likeT: LIM domain-likeF: Ribosomal_S26eECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A [auth 6]PF18005eIF3 subunit M, C-terminal helix (eIF3m_C_helix)eIF3 subunit M, C-terminal helixThis is the C-terminal helix domain found in Eukaryotic translation initiation factor 3 subunit M (eIF3m). In mammalian eIF3a, the C-terminal helix following the PCI domain is involved in interactions with other core subunits [1]. Domain
A [auth 6]PF01399PCI domain (PCI)PCI domainThis domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) [1]. Domain
PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
I [auth K]PF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- 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
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
O [auth P]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
P [auth I]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
F [auth 8]PF19445C-terminal region of eIF3h (eIF3h_C)C-terminal region of eIF3h- Family
F [auth 8]PF01398JAB1/Mov34/MPN/PAD-1 ubiquitin protease (JAB)JAB1/Mov34/MPN/PAD-1 ubiquitin proteaseProteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or J ...Proteins with this domain are found in proteasome regulatory subunits, eukaryotic initiation factor 3 (eIF3) subunits and regulators of transcription factors. This domain is known as the MPN domain [3] and PAD-1-like domain [4], JABP1 domain [5] or JAMM domain [7]. These are metalloenzymes that function as the ubiquitin isopeptidase/ deubiquitinase in the ubiquitin-based signalling and protein turnover pathways in eukaryotes [7]. Versions of the domain in prokaryotic cognates of the ubiquitin-modification pathway are shown to have a similar role, and the archaeal protein from Haloferax volcanii is found to cleave ubiquitin-like small archaeal modifier proteins (SAMP1/2) from protein conjugates [8,9].
Domain
B [auth 4]PF13012Maintenance of mitochondrial structure and function (MitMem_reg)Maintenance of mitochondrial structure and function- Family
R [auth 3]PF10075CSN8/PSMD8/EIF3K family (CSN8_PSD8_EIF3K)CSN8/PSMD8/EIF3K family- Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 6]Eukaryotic translation initiation factor 3 subunit M
C [auth u]Eukaryotic translation initiation factor 3 subunit A
40S ribosomal protein S7
40S ribosomal protein S27
I [auth K]40S ribosomal protein S21
K [auth L]40S ribosomal protein S2
L [auth O]40S ribosomal protein S3a
M [auth N]40S ribosomal protein SA
O [auth P]40S ribosomal protein S14
P [auth I]40S ribosomal protein S13
F [auth 8]Eukaryotic translation initiation factor 3 subunit H
E [auth y]Eukaryotic translation initiation factor 3 subunit C
D [auth v]Eukaryotic translation initiation factor 3 subunit E
B [auth 4]Eukaryotic translation initiation factor 3 subunit F
S [auth 5]Eukaryotic translation initiation factor 3 subunit L
R [auth 3]Eukaryotic translation initiation factor 3 subunit K
Q [auth x]Eukaryotic translation initiation factor 3 subunit D
N [auth Q]40S ribosomal protein S26
J [auth M]40S ribosomal protein S17

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A [auth 6]IPR016024Armadillo-type foldHomologous Superfamily
A [auth 6]IPR040750eIF3 subunit M, C-terminal helix domainDomain
A [auth 6]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
A [auth 6]IPR027528Eukaryotic translation initiation factor 3 subunit MFamily
A [auth 6]IPR045237Eukaryotic translation initiation factor 3 subunit M eIF3m/COP9 signalosome complex subunit 7 COPS7Family
A [auth 6]IPR000717Proteasome component (PCI) domainDomain
C [auth u]IPR027512Eukaryotic translation initiation factor 3 subunit AFamily
C [auth u]IPR054711eIF3a, PCI domain, TPR-like regionDomain
C [auth u]IPR000717Proteasome component (PCI) domainDomain
IPR000554Small ribosomal subunit protein eS7Family
IPR047861Small ribosomal subunit protein eS7, conserved siteConserved Site
IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
IPR000592Small ribosomal subunit protein eS27Family
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
I [auth K]IPR038579Small ribosomal subunit protein eS21 superfamilyHomologous Superfamily
I [auth K]IPR018279Small ribosomal subunit protein eS21, conserved siteConserved Site
I [auth K]IPR001931Small ribosomal subunit protein eS21Family
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
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
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
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
P [auth I]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
P [auth I]IPR000589Small ribosomal subunit protein uS15Family
P [auth I]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
P [auth I]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotaFamily
F [auth 8]IPR027524Eukaryotic translation initiation factor 3 subunit HFamily
F [auth 8]IPR045810eIF3h, C-terminalDomain
F [auth 8]IPR050242JAMM/MPN+ metalloenzymes, peptidase M67AFamily
F [auth 8]IPR037518MPN domainDomain
F [auth 8]IPR000555JAB1/MPN/MOV34 metalloenzyme domainDomain
E [auth y]IPR008905Eukaryotic translation initiation factor 3 subunit C, N-terminal domainDomain
E [auth y]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
E [auth y]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
E [auth y]IPR027516Eukaryotic translation initiation factor 3 subunit CFamily
E [auth y]IPR000717Proteasome component (PCI) domainDomain
D [auth v]IPR016650Eukaryotic translation initiation factor 3 subunit EFamily
D [auth v]IPR019010Eukaryotic translation initiation factor 3 subunit E, N-terminalDomain
D [auth v]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
D [auth v]IPR000717Proteasome component (PCI) domainDomain
B [auth 4]IPR027531Eukaryotic translation initiation factor 3 subunit FFamily
B [auth 4]IPR024969EIF3F/CSN6-like, C-terminalDomain
B [auth 4]IPR037518MPN domainDomain
B [auth 4]IPR000555JAB1/MPN/MOV34 metalloenzyme domainDomain
S [auth 5]IPR011990Tetratricopeptide-like helical domain superfamilyHomologous Superfamily
S [auth 5]IPR000717Proteasome component (PCI) domainDomain
S [auth 5]IPR019382Translation initiation factor 3 complex subunit LFamily
R [auth 3]IPR016024Armadillo-type foldHomologous Superfamily
R [auth 3]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
R [auth 3]IPR033464CSN8/PSMD8/EIF3KDomain
R [auth 3]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
R [auth 3]IPR016020Translation initiation factor 3, subunit 12, N-terminal, eukaryoticHomologous Superfamily
R [auth 3]IPR000717Proteasome component (PCI) domainDomain
R [auth 3]IPR009374Eukaryotic translation initiation factor 3 subunit KFamily
Q [auth x]IPR007783Eukaryotic translation initiation factor 3 subunit DFamily
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
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

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
A [auth 6]PharosQ7L2H7
C [auth u]PharosQ14152
PharosP62081
PharosP42677
I [auth K]PharosP63220
K [auth L]PharosP15880
M [auth N]PharosP08865
O [auth P]PharosP62263
P [auth I]PharosP62277
F [auth 8]PharosO15372
E [auth y]PharosQ99613
D [auth v]PharosP60228
B [auth 4]PharosO00303
R [auth 3]PharosQ9UBQ5
Q [auth x]PharosO15371
N [auth Q]PharosP62854
J [auth M]PharosP08708