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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8CAS

Cryo-EM structure of native Otu2-bound ubiquitinated 48S initiation complex (partial)

Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1P40S ribosomal protein S0-Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
In PDB		Saccharomyces cerevisiae W303Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A
2Q40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae W303RP10A,Small ribosomal subunit protein eS1-A
3R40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae W303Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
4S40S ribosomal protein S4-Bpolymer26129469.31UniProt (P0CX36)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
In PDB		Saccharomyces cerevisiae W303RP5,S7,Small ribosomal subunit protein eS4-B,YS6
5T40S ribosomal protein S6-Bpolymer23627054.51UniProt (P0CX38)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae W303RP9,S10,Small ribosomal subunit protein eS6-B,YS4
6V40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae W303
7W40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae W303
8X40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae W303
9Y40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae W303S27a,Small ribosomal subunit protein uS15,YS15
10Z40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae W303
11a40S ribosomal protein S21-Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae W303S26,Small ribosomal subunit protein eS21-A,YS25
12b40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae W303
13c40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae W303RP37,S28,Small ribosomal subunit protein uS12-A,YS14
14d40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae W303RP50,Small ribosomal subunit protein eS24-A
15e40S ribosomal protein S26-Apolymer11913538.91UniProt (P39938)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS26-A
16f40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae W303RP61,Small ribosomal subunit protein eS27-A,YS20
17g40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS30-A
18ERPS15 isoform 1polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae W303
19B40S ribosomal protein S3polymer24026542.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae W303RP13,Small ribosomal subunit protein uS3,YS3
20D40S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS10-A
21F40S ribosomal protein S12polymer14315488.61UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS12
22H40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae W303RP61R,Small ribosomal subunit protein uS9-A
23I40S ribosomal protein S17-Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae W303RP51A,Small ribosomal subunit protein eS17-A
24J40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein uS13-A
25K40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae W303RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
26L40S ribosomal protein S20polymer12113929.01UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae W303Small ribosomal subunit protein uS10
27M40S ribosomal protein S25-Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae W303RP45,S31,Small ribosomal subunit protein eS25-A,YS23
28NRPS29A isoform 1polymer566675.71UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae W303
29O40S ribosomal protein S31polymer768703.51UniProt (P05759)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae W303CEP76,S37,Small ribosomal subunit protein eS31,YS24
30hGuanine nucleotide-binding protein subunit beta-like proteinpolymer31934841.21UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae W303Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
31i40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae W303S33,Small ribosomal subunit protein eS28-A,YS27
32lEukaryotic translation initiation factor 3 subunit Ipolymer34738803.41UniProt (A0A6A5PTA5)
Pfam (PF00400)
UniProt (by SIFTS) (P40217)
In PDB		Saccharomyces cerevisiae W303
33rEukaryotic translation initiation factor 3 subunit Gpolymer27430547.51UniProt (A0A8H8UNW9)
Pfam (PF12353)
Pfam (PF00076)
UniProt (by SIFTS) (Q04067)
In PDB		Saccharomyces cerevisiae W303
341tRNApolymer7524713.01Saccharomyces cerevisiae W303
35mTIF5 isoform 1polymer40545322.01UniProt (A0A6A5Q3C7)
Pfam (PF01873)
Pfam (PF02020)
UniProt (by SIFTS) (P38431)
In PDB		Saccharomyces cerevisiae W303
36oEukaryotic translation initiation factor 3 subunit Apolymer964110517.61UniProt (P38249)
In PDB		Saccharomyces cerevisiae W303eIF3a,Eukaryotic translation initiation factor 3 110 kDa subunit homolog,eIF3 p110,Translation initiation factor eIF3,p110 subunit homolog
37pEukaryotic translation initiation factor 3 subunit Bpolymer76388241.81UniProt (A0A8H4F8W9)
Pfam (PF00076)
Pfam (PF08662)
UniProt (by SIFTS) (P06103)
In PDB		Saccharomyces cerevisiae W303
38qEukaryotic translation initiation factor 3 subunit Cpolymer81293310.21UniProt (A0A8H4BZ29)
Pfam (PF05470)
Pfam (PF01399)
UniProt (by SIFTS) (P32497)
In PDB		Saccharomyces cerevisiae W303
393mRNApolymer82534.61Saccharomyces cerevisiae
40AEukaryotic translation initiation factor 4Cpolymer15317462.21UniProt (A0A6A5PU90)
Pfam (PF01176)
UniProt (by SIFTS) (P38912)
In PDB		Saccharomyces cerevisiae W303
41kRLI1 isoform 1polymer60868433.21UniProt (A0A6A5Q259)
Pfam (PF04068)
Pfam (PF00037)
Pfam (PF00005)
UniProt (by SIFTS) (Q03195)
In PDB		Saccharomyces cerevisiae W303
42218S ribosomal RNApolymer1800579761.91Saccharomyces cerevisiae W303
43C40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae W303RP14,S2,Small ribosomal subunit protein uS7,YS8
44y60S ribosomal protein L40-Apolymer768576.81UniProt (P0CH08)
Pfam (PF00240)
In PDB		Saccharomyces cerevisiae W303CEP52,Large ribosomal subunit protein eL40-A
45n60S ribosomal protein L41-Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae W303L47,Large ribosomal subunit protein eL41-A,YL41
46jSUI2 isoform 1polymer30434763.71UniProt (A0A6A5PWU9)
Pfam (PF00575)
Pfam (PF07541)
UniProt (by SIFTS) (P20459)
In PDB		Saccharomyces cerevisiae W303
47Gprotein-synthesizing GTPasepolymer52757942.71UniProt (A0A6A5Q017)
Pfam (PF09173)
Pfam (PF00009)
Pfam (PF03144)
UniProt (by SIFTS) (P32481)
In PDB		Saccharomyces cerevisiae W303
48sSUI3 isoform 1polymer28531631.31UniProt (A0A8H4BUS5)
Pfam (PF01873)
UniProt (by SIFTS) (P09064)
In PDB		Saccharomyces cerevisiae W303
49xOTU domain-containing protein 2polymer30736157.01UniProt (P38747)
Pfam (PF02338)
In PDB		Saccharomyces cerevisiae W303
50U40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae W303RP30,RP40,Small ribosomal subunit protein eS7-A
51m, s, N, OZINC IONnon-polymer65.44Chemie (ZN)
52kADENOSINE-5'-DIPHOSPHATEnon-polymer427.21Chemie (ADP)
53k, 2, GMAGNESIUM IONnon-polymer24.35Chemie (MG)
54kADENOSINE-5'-TRIPHOSPHATEnon-polymer507.21Chemie (ATP)
55kIRON/SULFUR CLUSTERnon-polymer351.62Chemie (SF4)
56GMETHIONINEnon-polymer149.21Chemie (MET)
57GPHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTERnon-polymer521.21Chemie (GCP)
Sequence modifications
y: 1 - 76 (UniProt: P0CH08)
PDBExternal DatabaseDetails
Pro 19Ser 19conflict
Glu 24Asp 24conflict
Ala 28Ser 28conflict
x: 1 - 307 (UniProt: P38747)
PDBExternal DatabaseDetails
Ser 178Cys 178engineered mutation
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains50
Total formula weight1858873.1
Non-Polymers*Number of molecules15
Total formula weight2691.2
All*Total formula weight1861564.3
*Water molecules are not included.

220113

PDB entries from 2024-05-22

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