8ZDB

Cryo-EM structure of the human ubiquitylated 40S ribosome with RIOK3


Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B [auth A]PF00318Ribosomal protein S2 (Ribosomal_S2)Ribosomal protein S2- Family
B [auth A]PF1612240S ribosomal protein SA C-terminus (40S_SA_C)40S ribosomal protein SA C-terminus- Family
PF00900Ribosomal family S4e (Ribosomal_S4e)Ribosomal family S4e- Family
PF1612140S ribosomal protein S4 C-terminus (40S_S4_C)40S ribosomal protein S4 C-terminus- Family
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
PF00467KOW motif (KOW)KOW motif- Family
F [auth G]PF01092Ribosomal protein S6e (Ribosomal_S6e)Ribosomal protein S6e- Family
F [auth G]PF00400WD domain, G-beta repeat (WD40)WD domain, G-beta repeat- Repeat
H [auth I]PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...Domain
H [auth I]PF01201Ribosomal protein S8e (Ribosomal_S8e)Ribosomal protein S8e- Family
I [auth J]PF00240Ubiquitin family (ubiquitin)Ubiquitin familyThis family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...Domain
I [auth J]PF00163Ribosomal protein S4/S9 N-terminal domain (Ribosomal_S4)Ribosomal protein S4/S9 N-terminal domain- Family
I [auth J]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 ...Domain
L [auth O]PF00411Ribosomal protein S11 (Ribosomal_S11)Ribosomal protein S11- Family
M [auth V]PF01249Ribosomal protein S21e (Ribosomal_S21e)Ribosomal protein S21e- Family
P [auth Y]PF01282Ribosomal protein S24e (Ribosomal_S24e)Ribosomal protein S24e- Family
X [auth K]PF03501Plectin/S10 domain (S10_plectin)Plectin/S10 domainThis presumed domain is found at the N-terminus of some isoforms of the cytoskeletal muscle protein plectin as well as the ribosomal S10 protein. This domain may be involved in RNA binding. Domain
Z [auth P]PF00203Ribosomal protein S19 (Ribosomal_S19)Ribosomal protein S19Domain
CA [auth S]PF00416Ribosomal protein S13/S18 (Ribosomal_S13)Ribosomal protein S13/S18- Family
J [auth L]PF16205Ribosomal_S17 N-terminal (Ribosomal_S17_N)Ribosomal_S17 N-terminal- Family
J [auth L]PF00366Ribosomal protein S17 (Ribosomal_S17)Ribosomal protein S17Domain
K [auth N]PF00312Ribosomal protein S15 (Ribosomal_S15)Ribosomal protein S15Domain
N [auth W]PF00410Ribosomal protein S8 (Ribosomal_S8)Ribosomal protein S8Domain
O [auth X]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
V [auth D]PF07650KH domain (KH_2)KH domainDomain
V [auth D]PF00253Ribosomal protein S14p/S29e (Ribosomal_S14)Ribosomal protein S14p/S29e- Family
V [auth D]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
W [auth F]PF00177Ribosomal protein S7p/S5e (Ribosomal_S7)Ribosomal protein S7p/S5eThis family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. Domain
W [auth F]PF01599Ribosomal protein S27a (Ribosomal_S27)Ribosomal protein S27aThis family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesised as a C-terminal extension of ubiquitin (CEP). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins ...Domain
Y [auth M]PF01248Ribosomal protein L7Ae/L30e/S12e/Gadd45 family (Ribosomal_L7Ae)Ribosomal protein L7Ae/L30e/S12e/Gadd45 familyThis family includes: Ribosomal L7A from metazoa, Ribosomal L8-A and L8-B from fungi, 30S ribosomal protein HS6 from archaebacteria, 40S ribosomal protein S12 from eukaryotes, Ribosomal protein L30 from eukaryotes and archaebacteria. Gadd45 and MyD11 ...Domain
AA [auth Q]PF00380Ribosomal protein S9/S16 (Ribosomal_S9)Ribosomal protein S9/S16- Family
C [auth B]PF01667Ribosomal protein S27 (Ribosomal_S27e)Ribosomal protein S27- Family
DA [auth T]PF01090Ribosomal protein S19e (Ribosomal_S19e)Ribosomal protein S19e- Family
EA [auth U]PF00338Ribosomal protein S10p/S20e (Ribosomal_S10)Ribosomal protein S10p/S20eThis family includes small ribosomal subunit S10 from prokaryotes and S20 from eukaryotes. Domain
D [auth C]PF03719Ribosomal protein S5, C-terminal domain (Ribosomal_S5_C)Ribosomal protein S5, C-terminal domainDomain
D [auth C]PF00333Ribosomal protein S5, N-terminal domain (Ribosomal_S5)Ribosomal protein S5, N-terminal domainDomain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A [auth 2]18S rRNA---
B [auth A]Small ribosomal subunit protein uS2
Small ribosomal subunit protein eS4, X isoform
F [auth G]Small ribosomal subunit protein eS6
H [auth I]Small ribosomal subunit protein eS8
I [auth J]Small ribosomal subunit protein uS4
L [auth O]Small ribosomal subunit protein uS11
M [auth V]Small ribosomal subunit protein eS21
P [auth Y]Small ribosomal subunit protein eS24
R [auth b]Small ribosomal subunit protein eS27
T [auth e]Small ribosomal subunit protein eS30
U [auth h]Small ribosomal subunit protein eS32
X [auth K]Small ribosomal subunit protein eS10
Z [auth P]Small ribosomal subunit protein uS19
BA [auth R]Small ribosomal subunit protein eS17
CA [auth S]Small ribosomal subunit protein uS13
GA [auth c]Small ribosomal subunit protein eS28
IA [auth g]Small ribosomal subunit protein RACK1
J [auth L]Small ribosomal subunit protein uS17
K [auth N]Small ribosomal subunit protein uS15
N [auth W]Small ribosomal subunit protein uS8
O [auth X]Small ribosomal subunit protein uS12
Q [auth a]Small ribosomal subunit protein eS26
S [auth d]Small ribosomal subunit protein uS14
V [auth D]Small ribosomal subunit protein uS3
W [auth F]Small ribosomal subunit protein uS7
Y [auth M]Small ribosomal subunit protein eS12
AA [auth Q]Small ribosomal subunit protein uS9
C [auth B]Small ribosomal subunit protein eS1
DA [auth T]Small ribosomal subunit protein eS19
EA [auth U]Small ribosomal subunit protein uS10
FA [auth Z]Small ribosomal subunit protein eS25
HA [auth f],
KA [auth i],
LA [auth j]
Ubiquitin
JA [auth p]Serine/threonine-protein kinase RIO3
D [auth C]Small ribosomal subunit protein uS5
G [auth H]Small ribosomal subunit protein eS7

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
B [auth A]IPR023591Small ribosomal subunit protein uS2, flavodoxin-like domain superfamilyHomologous Superfamily
B [auth A]IPR001865Small ribosomal subunit protein uS2Family
B [auth A]IPR032281Small ribosomal subunit protein uS2, C-terminal domainDomain
B [auth A]IPR027504Small ribosomal subunit protein uS2, vertebratesFamily
B [auth A]IPR005707Small ribosomal subunit protein uS2, eukaryotic/archaealFamily
B [auth A]IPR018130Small ribosomal subunit protein uS2, conserved siteConserved Site
B [auth A]IPR027498Small ribosomal subunit protein uS2, eukaryoticFamily
IPR013843Small ribosomal subunit protein eS4, N-terminalDomain
IPR032277Small ribosomal subunit protein eS4, C-terminal domainDomain
IPR013845Small ribosomal subunit protein eS4, central regionDomain
IPR014722Large ribosomal subunit protein uL2, domain 2Homologous Superfamily
IPR041982Small ribosomal subunit protein eS4, KOW domainDomain
IPR018199Small ribosomal subunit protein eS4, N-terminal, conserved siteConserved Site
IPR002942RNA-binding S4 domainDomain
IPR000876Small ribosomal subunit protein eS4Family
IPR038237Small ribosomal subunit protein eS4, central domain superfamilyHomologous Superfamily
IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
IPR005824KOWDomain
F [auth G]IPR018282Small ribosomal subunit protein eS6, conserved siteConserved Site
F [auth G]IPR001377Small ribosomal subunit protein eS6Family
F [auth G]IPR014401Small ribosomal subunit protein eS6-likeFamily
H [auth I]IPR042563Small ribosomal subunit protein eS8 subdomain, eukaryotesHomologous Superfamily
H [auth I]IPR022309Ribosomal protein eS8/ribosomal biogenesis NSA2Family
H [auth I]IPR018283Small ribosomal subunit protein eS8, conserved siteConserved Site
H [auth I]IPR001047Small ribosomal subunit protein eS8Family
I [auth J]IPR002942RNA-binding S4 domainDomain
I [auth J]IPR022801Small ribosomal subunit protein uS4Family
I [auth J]IPR018079Small ribosomal subunit protein uS4, conserved siteConserved Site
I [auth J]IPR001912Small ribosomal subunit protein uS4, N-terminalDomain
I [auth J]IPR005710Small ribosomal subunit protein uS4, eukaryotic/archaealFamily
I [auth J]IPR036986RNA-binding S4 domain superfamilyHomologous Superfamily
L [auth O]IPR036967Small ribosomal subunit protein uS11 superfamilyHomologous Superfamily
L [auth O]IPR018102Small ribosomal subunit protein uS11, conserved siteConserved Site
L [auth O]IPR001971Small ribosomal subunit protein uS11Family
M [auth V]IPR038579Small ribosomal subunit protein eS21 superfamilyHomologous Superfamily
M [auth V]IPR018279Small ribosomal subunit protein eS21, conserved siteConserved Site
M [auth V]IPR001931Small ribosomal subunit protein eS21Family
P [auth Y]IPR053709Eukaryotic Ribosomal Protein eS24Homologous Superfamily
P [auth Y]IPR001976Small ribosomal subunit protein eS24Family
P [auth Y]IPR012678Ribosomal protein uL23/eL15/eS24 core domain superfamilyHomologous Superfamily
P [auth Y]IPR018098Small ribosomal subunit protein eS24 conserved siteConserved Site
R [auth b]IPR023407Small ribosomal subunit protein eS27, zinc-binding domain superfamilyHomologous Superfamily
R [auth b]IPR000592Small ribosomal subunit protein eS27Family
R [auth b]IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
T [auth e]IPR019954Ubiquitin conserved siteConserved Site
T [auth e]IPR000626Ubiquitin-like domainDomain
T [auth e]IPR006846Small ribosomal subunit protein eS30Family
T [auth e]IPR039415Ubiquitin-like protein FUBIDomain
T [auth e]IPR019956Ubiquitin domainDomain
T [auth e]IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
U [auth h]IPR007836Large ribosomal subunit protein eS32Family
X [auth K]IPR037447Small ribosomal subunit protein eS10Family
X [auth K]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
X [auth K]IPR005326Plectin/eS10, N-terminalDomain
Z [auth P]IPR023575Small ribosomal subunit protein uS19, superfamilyHomologous Superfamily
Z [auth P]IPR020934Small ribosomal subunit protein uS19, conserved siteConserved Site
Z [auth P]IPR005713Small ribosomal subunit protein uS19, eukaryotic/archaealFamily
Z [auth P]IPR002222Small ribosomal subunit protein uS19Family
BA [auth R]IPR001210Small ribosomal subunit protein eS17Family
BA [auth R]IPR036401Small ribosomal subunit protein eS17 superfamilyHomologous Superfamily
BA [auth R]IPR018273Small ribosomal subunit protein eS17, conserved siteConserved Site
CA [auth S]IPR018269Small ribosomal subunit protein uS13, conserved siteConserved Site
CA [auth S]IPR027437Small ribosomal subunit protein uS13, C-terminalHomologous Superfamily
CA [auth S]IPR001892Small ribosomal subunit protein uS13Family
CA [auth S]IPR010979Small ribosomal subunit protein uS13-like, H2THHomologous Superfamily
GA [auth c]IPR028626Ribosomal protein eS28 conserved siteConserved Site
GA [auth c]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
GA [auth c]IPR000289Small ribosomal subunit protein eS28Family
IA [auth g]IPR019775WD40 repeat, conserved siteConserved Site
IA [auth g]IPR036322WD40-repeat-containing domain superfamilyHomologous Superfamily
IA [auth g]IPR045223Small ribosomal subunit protein RACK1-likeFamily
IA [auth g]IPR020472G-protein beta WD-40 repeatRepeat
IA [auth g]IPR015943WD40/YVTN repeat-like-containing domain superfamilyHomologous Superfamily
IA [auth g]IPR001680WD40 repeatRepeat
J [auth L]IPR019979Small ribosomal subunit protein uS17, conserved siteConserved Site
J [auth L]IPR032440Small ribosomal subunit protein uS17, N-terminalDomain
J [auth L]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
J [auth L]IPR000266Small ribosomal subunit protein uS17Family
J [auth L]IPR028333Small ribosomal subunit protein uS17, archaeal/eukaryoticFamily
K [auth N]IPR009068uS15/NS1, RNA-binding domain superfamilyHomologous Superfamily
K [auth N]IPR000589Small ribosomal subunit protein uS15Family
K [auth N]IPR023029Small ribosomal subunit protein uS15, archaea/eukaryotesFamily
K [auth N]IPR012606Small ribosomal subunit protein uS15, N-terminalDomain
N [auth W]IPR047863Small ribosomal subunit protein uS8, conserved siteConserved Site
N [auth W]IPR000630Small ribosomal subunit protein uS8Family
N [auth W]IPR035987Small ribosomal subunit protein uS8 superfamilyHomologous Superfamily
O [auth X]IPR006032Small ribosomal subunit protein uS12Family
O [auth X]IPR012340Nucleic acid-binding, OB-foldHomologous Superfamily
O [auth X]IPR005680Small ribosomal subunit protein uS12, eukaryotic/archaealFamily
Q [auth a]IPR047864Ribosomal protein eS26, conserved siteConserved Site
Q [auth a]IPR038551Ribosomal protein eS26 superfamilyHomologous Superfamily
Q [auth a]IPR000892Small ribosomal subunit protein eS26Family
S [auth d]IPR018271Small ribosomal subunit protein uS14, conserved siteConserved Site
S [auth d]IPR043140Small ribosomal subunit protein uS14 superfamilyHomologous Superfamily
S [auth d]IPR001209Small ribosomal subunit protein uS14Family
S [auth d]IPR039744Small ribosomal subunit protein uS14, eukaryotes/archaeaFamily
V [auth D]IPR009019K homology domain superfamily, prokaryotic typeHomologous Superfamily
V [auth D]IPR015946K homology domain-like, alpha/betaHomologous Superfamily
V [auth D]IPR036419Ribosomal protein S3, C-terminal domain superfamilyHomologous Superfamily
V [auth D]IPR004044K Homology domain, type 2Domain
V [auth D]IPR001351Small ribosomal subunit protein uS3, C-terminalDomain
V [auth D]IPR005703Small ribosomal subunit protein uS3, eukaryotic/archaealFamily
V [auth D]IPR018280Small ribosomal subunit protein uS3, conserved siteConserved Site
W [auth F]IPR023798Small ribosomal subunit protein uS7 domainDomain
W [auth F]IPR020606Small ribosomal subunit protein uS7, conserved siteConserved Site
W [auth F]IPR036823Small ribosomal subunit protein uS7 domain superfamilyHomologous Superfamily
W [auth F]IPR000235Small ribosomal subunit protein uS7Family
W [auth F]IPR005716Ribosomal protein uS7, eukaryotic/archaealFamily
Y [auth M]IPR000530Small ribosomal subunit protein eS12Family
Y [auth M]IPR004038Ribosomal protein eL8/eL30/eS12/Gadd45Domain
Y [auth M]IPR047860Small ribosomal subunit protein eS12, conserved siteConserved Site
Y [auth M]IPR029064Ribosomal protein eL30-like superfamilyHomologous Superfamily
AA [auth Q]IPR020574Small ribosomal subunit protein uS9, conserved siteConserved Site
AA [auth Q]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
AA [auth Q]IPR000754Small ribosomal subunit protein uS9Family
AA [auth Q]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
C [auth B]IPR001593Small ribosomal subunit protein eS1Family
C [auth B]IPR018281Small ribosomal subunit protein eS1, conserved siteConserved Site
C [auth B]IPR027500Small ribosomal subunit protein eS1, eukaryotesFamily
DA [auth T]IPR018277Small ribosomal subunit protein eS19, conserved siteConserved Site
DA [auth T]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
DA [auth T]IPR036390Winged helix DNA-binding domain superfamilyHomologous Superfamily
DA [auth T]IPR001266Small ribosomal subunit protein eS19Family
EA [auth U]IPR027486Small ribosomal subunit protein uS10 domainDomain
EA [auth U]IPR036838Small ribosomal subunit protein uS10 domain superfamilyHomologous Superfamily
EA [auth U]IPR005729Small ribosomal subunit protein uS10, eukaryotic/archaealFamily
EA [auth U]IPR018268Small ribosomal subunit protein uS10, conserved siteConserved Site
EA [auth U]IPR001848Small ribosomal subunit protein uS10Family
FA [auth Z]IPR036388Winged helix-like DNA-binding domain superfamilyHomologous Superfamily
FA [auth Z]IPR004977Small ribosomal subunit protein eS25Family
HA [auth f],
KA [auth i],
LA [auth j]
IPR019954Ubiquitin conserved siteConserved Site
HA [auth f],
KA [auth i],
LA [auth j]
IPR050158Ubiquitin and ubiquitin-likeFamily
HA [auth f],
KA [auth i],
LA [auth j]
IPR011332Zinc-binding ribosomal proteinHomologous Superfamily
HA [auth f],
KA [auth i],
LA [auth j]
IPR000626Ubiquitin-like domainDomain
HA [auth f],
KA [auth i],
LA [auth j]
IPR038582Small ribosomal subunit protein eS31 eukaryotic-type superfamilyHomologous Superfamily
HA [auth f],
KA [auth i],
LA [auth j]
IPR002906Small ribosomal subunit protein eS31Domain
HA [auth f],
KA [auth i],
LA [auth j]
IPR019956Ubiquitin domainDomain
HA [auth f],
KA [auth i],
LA [auth j]
IPR029071Ubiquitin-like domain superfamilyHomologous Superfamily
JA [auth p]IPR018935RIO kinase, conserved siteConserved Site
JA [auth p]IPR000687RIO kinaseDomain
JA [auth p]IPR011009Protein kinase-like domain superfamilyHomologous Superfamily
JA [auth p]IPR051272RIO-type Ser/Thr kinaseFamily
JA [auth p]IPR017406Serine/threonine-protein kinase Rio3Family
D [auth C]IPR020568Ribosomal protein uS5 domain 2-type superfamilyHomologous Superfamily
D [auth C]IPR018192Small ribosomal subunit protein uS5, N-terminal, conserved siteConserved Site
D [auth C]IPR014721Small ribosomal subunit protein uS5 domain 2-type fold, subgroupHomologous Superfamily
D [auth C]IPR000851Small ribosomal subunit protein uS5Family
D [auth C]IPR005711Small ribosomal subunit protein uS5, eukaryotic/archaealFamily
D [auth C]IPR005324Small ribosomal subunit protein uS5, C-terminalDomain
D [auth C]IPR013810Small ribosomal subunit protein uS5, N-terminalDomain
G [auth H]IPR000554Small ribosomal subunit protein eS7Family
G [auth H]IPR047861Small ribosomal subunit protein eS7, conserved siteConserved Site

Pharos: Disease Associations Pharos Homepage Annotation

ChainsDrug Target  Associated Disease
B [auth A]PharosP08865
PharosP62701
F [auth G]PharosP62753
H [auth I]PharosP62241
I [auth J]PharosP46781
L [auth O]PharosP62263
M [auth V]PharosP63220
P [auth Y]PharosP62847
R [auth b]PharosP42677
T [auth e]PharosP62861
U [auth h]PharosP62945
X [auth K]PharosP46783
Z [auth P]PharosP62841
BA [auth R]PharosP08708
CA [auth S]PharosP62269
GA [auth c]PharosP62857
IA [auth g]PharosP63244
J [auth L]PharosP62280
K [auth N]PharosP62277
N [auth W]PharosP62244
O [auth X]PharosP62266
Q [auth a]PharosP62854
S [auth d]PharosP62273
V [auth D]PharosP23396
W [auth F]PharosP46782
Y [auth M]PharosP25398
AA [auth Q]PharosP62249
DA [auth T]PharosP39019
EA [auth U]PharosP60866
FA [auth Z]PharosP62851
HA [auth f],
KA [auth i],
LA [auth j]
PharosP62979
JA [auth p]PharosO14730
D [auth C]PharosP15880
G [auth H]PharosP62081