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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

8CAS

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

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(P)		40S ribosomal protein S0-Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae W303Nucleic acid-binding protein NAB1A,Small ribosomal subunit protein uS2-A
2B
(Q)		40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)		Saccharomyces cerevisiae W303RP10A,Small ribosomal subunit protein eS1-A
3C
(R)		40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae W303Omnipotent suppressor protein SUP44,RP12,S4,Small ribosomal subunit protein uS5,YS5
4D
(S)		40S ribosomal protein S4-Bpolymer26129469.31UniProt (P0CX36)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)		Saccharomyces cerevisiae W303RP5,S7,Small ribosomal subunit protein eS4-B,YS6
5E
(T)		40S ribosomal protein S6-Bpolymer23627054.51UniProt (P0CX38)
Pfam (PF01092)		Saccharomyces cerevisiae W303RP9,S10,Small ribosomal subunit protein eS6-B,YS4
6F
(V)		40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae W303
7G
(W)		40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae W303
8H
(X)		40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae W303
9I
(Y)		40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae W303S27a,Small ribosomal subunit protein uS15,YS15
10J
(Z)		40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)		Saccharomyces cerevisiae W303
11K
(a)		40S ribosomal protein S21-Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae W303S26,Small ribosomal subunit protein eS21-A,YS25
12L
(b)		40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae W303
13M
(c)		40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae W303RP37,S28,Small ribosomal subunit protein uS12-A,YS14
14N
(d)		40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae W303RP50,Small ribosomal subunit protein eS24-A
15O
(e)		40S ribosomal protein S26-Apolymer11913538.91UniProt (P39938)
Pfam (PF01283)		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS26-A
16P
(f)		40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae W303RP61,Small ribosomal subunit protein eS27-A,YS20
17Q
(g)		40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS30-A
18R
(E)		RPS15 isoform 1polymer14216031.91UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae W303
19S
(B)		40S ribosomal protein S3polymer24026542.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae W303RP13,Small ribosomal subunit protein uS3,YS3
20T
(D)		40S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS10-A
21U
(F)		40S ribosomal protein S12polymer14315488.61UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae W303Small ribosomal subunit protein eS12
22V
(H)		40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae W303RP61R,Small ribosomal subunit protein uS9-A
23W
(I)		40S ribosomal protein S17-Apolymer13615820.41UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae W303RP51A,Small ribosomal subunit protein eS17-A
24X
(J)		40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae W303Small ribosomal subunit protein uS13-A
25Y
(K)		40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae W303RP55A,S16a,Small ribosomal subunit protein eS19-A,YP45,YS16A
26Z
(L)		40S ribosomal protein S20polymer12113929.01UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae W303Small ribosomal subunit protein uS10
27AA
(M)		40S ribosomal protein S25-Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae W303RP45,S31,Small ribosomal subunit protein eS25-A,YS23
28BA
(N)		RPS29A isoform 1polymer566675.71UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae W303
29CA
(O)		40S ribosomal protein S31polymer768703.51UniProt (P05759)
Pfam (PF01599)		Saccharomyces cerevisiae W303CEP76,S37,Small ribosomal subunit protein eS31,YS24
30DA
(h)		Guanine nucleotide-binding protein subunit beta-like proteinpolymer31934841.21UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae W303Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1,Small ribosomal subunit protein RACK1
31EA
(i)		40S ribosomal protein S28-Apolymer677605.81UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae W303S33,Small ribosomal subunit protein eS28-A,YS27
32FA
(l)		Eukaryotic translation initiation factor 3 subunit Ipolymer34738803.41UniProt (A0A6A5PTA5)
Pfam (PF00400)
UniProt (by SIFTS) (P40217)		Saccharomyces cerevisiae W303
33GA
(r)		Eukaryotic translation initiation factor 3 subunit Gpolymer27430547.51UniProt (A0A8H8UNW9)
Pfam (PF12353)
Pfam (PF00076)
UniProt (by SIFTS) (Q04067)		Saccharomyces cerevisiae W303
34HA
(1)		tRNApolymer7524713.01Saccharomyces cerevisiae W303
35IA
(m)		TIF5 isoform 1polymer40545322.01UniProt (A0A6A5Q3C7)
Pfam (PF01873)
Pfam (PF02020)
UniProt (by SIFTS) (P38431)		Saccharomyces cerevisiae W303
36JA
(o)		Eukaryotic translation initiation factor 3 subunit Apolymer964110517.61UniProt (P38249)
Pfam (PF22591)		Saccharomyces cerevisiae W303eIF3a,Eukaryotic translation initiation factor 3 110 kDa subunit homolog,eIF3 p110,Translation initiation factor eIF3,p110 subunit homolog
37KA
(p)		Eukaryotic translation initiation factor 3 subunit Bpolymer76388241.81UniProt (A0A8H4F8W9)
Pfam (PF00076)
Pfam (PF08662)
UniProt (by SIFTS) (P06103)		Saccharomyces cerevisiae W303
38LA
(q)		Eukaryotic translation initiation factor 3 subunit Cpolymer81293310.21UniProt (A0A8H4BZ29)
Pfam (PF05470)
Pfam (PF01399)
UniProt (by SIFTS) (P32497)		Saccharomyces cerevisiae W303
39MA
(3)		mRNApolymer82534.61Saccharomyces cerevisiae
40NA
(A)		Eukaryotic translation initiation factor 4Cpolymer15317462.21UniProt (A0A6A5PU90)
Pfam (PF01176)
UniProt (by SIFTS) (P38912)		Saccharomyces cerevisiae W303
41OA
(k)		RLI1 isoform 1polymer60868433.21UniProt (A0A6A5Q259)
Pfam (PF04068)
Pfam (PF00037)
Pfam (PF00005)
UniProt (by SIFTS) (Q03195)		Saccharomyces cerevisiae W303
42PA
(2)		18S ribosomal RNApolymer1800579761.91Saccharomyces cerevisiae W303
43QA
(C)		40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae W303RP14,S2,Small ribosomal subunit protein uS7,YS8
44RA
(y)		60S ribosomal protein L40-Apolymer768576.81UniProt (P0CH08)
Pfam (PF00240)		Saccharomyces cerevisiae W303CEP52,Large ribosomal subunit protein eL40-A
45SA
(n)		60S ribosomal protein L41-Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)		Saccharomyces cerevisiae W303L47,Large ribosomal subunit protein eL41-A,YL41
46TA
(j)		SUI2 isoform 1polymer30434763.71UniProt (A0A6A5PWU9)
Pfam (PF00575)
Pfam (PF07541)
UniProt (by SIFTS) (P20459)		Saccharomyces cerevisiae W303
47UA
(G)		protein-synthesizing GTPasepolymer52757942.71UniProt (A0A6A5Q017)
Pfam (PF09173)
Pfam (PF00009)
Pfam (PF03144)
UniProt (by SIFTS) (P32481)		Saccharomyces cerevisiae W303
48VA
(s)		SUI3 isoform 1polymer28531631.31UniProt (A0A8H4BUS5)
Pfam (PF01873)
UniProt (by SIFTS) (P09064)		Saccharomyces cerevisiae W303
49WA
(x)		OTU domain-containing protein 2polymer30736157.01UniProt (P38747)
Pfam (PF02338)		Saccharomyces cerevisiae W303
50XA
(U)		40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae W303RP30,RP40,Small ribosomal subunit protein eS7-A
51AB, MB, YA, ZA
(m, s, N, O)		ZINC IONnon-polymer65.44Chemie (ZN)
52BB
(k)		ADENOSINE-5'-DIPHOSPHATEnon-polymer427.21Chemie (ADP)
53CB, EB, HB, IB, KB
(k, 2, G)		MAGNESIUM IONnon-polymer24.35Chemie (MG)
54DB
(k)		ADENOSINE-5'-TRIPHOSPHATEnon-polymer507.21Chemie (ATP)
55FB, GB
(k)		IRON/SULFUR CLUSTERnon-polymer351.62Chemie (SF4)
56JB
(G)		METHIONINEnon-polymer149.21Chemie (MET)
57LB
(G)		PHOSPHOMETHYLPHOSPHONIC 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.

247536

PDB entries from 2026-01-14

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