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5MC6

Cryo-EM structure of a native ribosome-Ski2-Ski3-Ski8 complex from S. cerevisiae

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A
(2)
18S ribosomal RNApolymer1800579761.91REF (831416132)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
2B
(A)
40S ribosomal protein S3polymer24026542.81UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP13,YS3
3C
(B)
40S ribosomal protein S5polymer22525072.61UniProt (P26783)
Pfam (PF00177)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP14,S2,YS8
4D
(C)
40S ribosomal protein S10-Apolymer10512757.41UniProt (Q08745)
Pfam (PF03501)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
5E
(D)
40S ribosomal protein S12polymer14315488.61UniProt (P48589)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
6F
(E)
40S ribosomal protein S15polymer14216031.91UniProt (Q01855)
Pfam (PF00203)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RIG protein,RP52,S21,YS21
7G
(F)
40S ribosomal protein S16-Apolymer14315877.51UniProt (P0CX51)
Pfam (PF00380)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61R
8H
(G)
40S ribosomal protein S17-Bpolymer13615835.41UniProt (P14127)
Pfam (PF00833)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP51B
9I
(H)
40S ribosomal protein S18-Apolymer14617071.61UniProt (P0CX55)
Pfam (PF00416)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
10J
(I)
40S ribosomal protein S19-Apolymer14415942.11UniProt (P07280)
Pfam (PF01090)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP55A,S16a,YP45,YS16A
11K
(J)
40S ribosomal protein S20polymer12113929.01UniProt (P38701)
Pfam (PF00338)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
12L
(K)
40S ribosomal protein S25-Apolymer10812067.31UniProt (Q3E792)
Pfam (PF03297)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP45,S31,YS23
13M
(L)
40S ribosomal protein S28-Bpolymer677578.81UniProt (P0C0X0)
Pfam (PF01200)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S33,YS27
14N
(M)
40S ribosomal protein S29-Apolymer566675.71UniProt (P41057)
Pfam (PF00253)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S36,YS29
15O
(N)
Ubiquitin-40S ribosomal protein S31polymer15217254.21UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
16P
(O)
Guanine nucleotide-binding protein subunit beta-like proteinpolymer31934841.21UniProt (P38011)
Pfam (PF00400)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Receptor for activated C kinase,Receptor of activated protein kinase C 1,RACK1
17Q
(P)
40S ribosomal protein S0-Apolymer25228051.31UniProt (P32905)
Pfam (PF00318)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Nucleic acid-binding protein NAB1A
18R
(Q)
40S ribosomal protein S1-Apolymer25528798.51UniProt (P33442)
Pfam (PF01015)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP10A
19S
(R)
40S ribosomal protein S2polymer25427490.81UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Omnipotent suppressor protein SUP44,RP12,S4,YS5
20T
(S)
40S ribosomal protein S4-Apolymer26129469.31UniProt (P0CX35)
Pfam (PF08071)
Pfam (PF01479)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP5,S7,YS6
21U
(T)
40S ribosomal protein S6-Apolymer23627054.51UniProt (P0CX37)
Pfam (PF01092)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP9,S10,YS4
22V
(U)
40S ribosomal protein S7-Apolymer19021658.21UniProt (P26786)
Pfam (PF01251)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP30,RP40
23W
(V)
40S ribosomal protein S8-Apolymer20022537.81UniProt (P0CX39)
Pfam (PF01201)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP19,S14,YS9
24X
(W)
40S ribosomal protein S9-Apolymer19722487.91UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP21,S13,YP28,YS11
25Y
(X)
40S ribosomal protein S11-Apolymer15617785.91UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP41,S18,YS12
26Z
(Y)
40S ribosomal protein S13polymer15117059.91UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S27a,YS15
27AA
(Z)
40S ribosomal protein S14-Apolymer13714562.71UniProt (P06367)
Pfam (PF00411)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP59A
28BA
(a)
40S ribosomal protein S21-Apolymer879758.81UniProt (P0C0V8)
Pfam (PF01249)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)S26,YS25
29CA
(b)
40S ribosomal protein S22-Apolymer13014650.11UniProt (P0C0W1)
Pfam (PF00410)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50,S24,YP58,YS22
30DA
(c)
40S ribosomal protein S23-Apolymer14516073.91UniProt (P0CX29)
Pfam (PF00164)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP37,S28,YS14
31EA
(d)
40S ribosomal protein S24-Apolymer13515362.81UniProt (P0CX31)
Pfam (PF01282)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP50
32FA
(e)
40S ribosomal protein S26-Apolymer11913538.91UniProt (P39938)
Pfam (PF01283)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
33GA
(f)
40S ribosomal protein S27-Apolymer828893.41UniProt (P35997)
Pfam (PF01667)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP61,YS20
34HA
(g)
40S ribosomal protein S30-Apolymer637137.51UniProt (P0CX33)
Pfam (PF04758)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
35IA
(l)
mRNApolymer3410494.91Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
36JA
(m)
A-site tRNApolymer7624378.41Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
37KA
(n)
P-site tRNApolymer7724815.71Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
38LA
(h)
Antiviral helicase SKI2polymer1287146259.11UniProt (P35207)
Pfam (PF17911)
Pfam (PF00270)
Pfam (PF00271)
Pfam (PF21408)
Pfam (PF21409)
Pfam (PF08148)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Superkiller protein 2
39MA
(i)
Superkiller protein 3polymer1432163922.11UniProt (P17883)
Pfam (PF18833)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
40NA, OA
(j, k)
Antiviral protein SKI8polymer39744283.52UniProt (Q02793)
Pfam (PF00400)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Superkiller protein 8
41PA
(AA)
60S ribosomal protein L8-Apolymer25628175.81UniProt (P17076)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L4,L4-2,L7a-1,Maintenance of killer protein 7,RP6,YL5
42QA
(AB)
60S ribosomal protein L23-Apolymer13714494.01UniProt (P0CX41)
Pfam (PF00238)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17a,YL32
43RA
(AC)
60S ribosomal protein L36-Apolymer10011151.31UniProt (P05745)
Pfam (PF01158)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L39,YL39
44SA
(AD)
60S ribosomal protein L9-Apolymer19121605.11UniProt (P05738)
Pfam (PF00347)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L8,RP24,YL11
45TA
(AE)
60S ribosomal protein L24-Apolymer15517661.71UniProt (P04449)
Pfam (PF01246)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L30,RP29,YL21
46UA
(AF)
60S ribosomal protein L37-Apolymer889877.41UniProt (P49166)
Pfam (PF01907)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L43,YL35,YP55
47VA
(AG)
60S ribosomal protein L11-Apolymer17419755.71UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L16,RP39,YL22
48WA
(AH)
60S ribosomal protein L25polymer14215787.61UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP16L,YL25,YP42'
49XA
(AI)
60S ribosomal protein L38polymer788845.61UniProt (P49167)
Pfam (PF01781)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
50YA
(AJ)
60S ribosomal protein L13-Apolymer19922604.21UniProt (Q12690)
Pfam (PF01294)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
51ZA
(AK)
60S ribosomal protein L26-Apolymer12714265.81UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L33,YL33
52AB
(AL)
60S ribosomal protein L39polymer516358.61UniProt (P04650)
Pfam (PF00832)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L46,YL40
53BB
(AM)
60S ribosomal protein L14-Apolymer13815195.11UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
54CB
(AN)
60S ribosomal protein L27-Apolymer13615568.41UniProt (P0C2H6)
Pfam (PF01777)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
55DB
(AO)
Ubiquitin-60S ribosomal protein L40polymer12814583.11UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
56EB
(AP)
60S ribosomal protein L42-Apolymer10612246.71UniProt (P0CX27)
Pfam (PF00935)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L41,YL27,YP44
57FB
(AQ)
60S ribosomal protein L15-Apolymer20424482.41UniProt (P05748)
Pfam (PF00827)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13,RP15R,YL10,YP18
58GB
(AR)
60S ribosomal protein L28polymer14916761.71UniProt (P02406)
Pfam (PF00828)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L27a,L29,RP44,RP62,YL24
59HB
(AS)
60S ribosomal protein L41-Apolymer253354.21UniProt (P0CX86)
Pfam (PF05162)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L47,YL41
60IB
(AT)
60S ribosomal protein L43-Apolymer9210113.01UniProt (P0CX25)
Pfam (PF01780)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37a,YL35
61JB
(AU)
60S ribosomal protein L16-Apolymer19922247.21UniProt (P26784)
Pfam (PF00572)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L13a,L21,RP22,YL15
62KB
(AV)
60S ribosomal protein L29polymer596691.91UniProt (P05747)
Pfam (PF01779)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)YL43
63LB
(AW)
60S ribosomal protein L2-Apolymer25427463.61UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L5,RP8,YL6
64MB
(AX)
60S ribosomal protein L17-Apolymer18420589.51UniProt (P05740)
Pfam (PF00237)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L20A,YL17
65NB
(AY)
60S ribosomal protein L30polymer10511430.41UniProt (P14120)
Pfam (PF01248)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L32,RP73,YL38
66OB
(AZ)
uL1polymer21017890.01Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
67PB
(BA)
60S ribosomal protein L3polymer38743850.81UniProt (P14126)
Pfam (PF00297)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)Maintenance of killer protein 8,RP1,Trichodermin resistance protein,YL1
68QB
(BB)
60S ribosomal protein L18-Apolymer18620609.31UniProt (P0CX49)
Pfam (PF17135)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)RP28
69RB
(BC)
60S ribosomal protein L31-Apolymer11312980.21UniProt (P0C2H8)
Pfam (PF01198)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L34,YL28
70SB
(BD)
60S ribosomal protein L10polymer22125410.51UniProt (P41805)
Pfam (PF00252)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L9,Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
71TB
(BE)
60S ribosomal protein L4-Apolymer36239159.11UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L2,RP2,YL2
72UB
(BF)
60S ribosomal protein L19-Apolymer18921762.31UniProt (P0CX82)
Pfam (PF01280)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L23,RP15L,RP33,YL14
73VB
(BG)
60S ribosomal protein L32polymer13014809.41UniProt (P38061)
Pfam (PF01655)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
74WB
(BH)
60S ribosomal protein L20-Apolymer17220478.91UniProt (P0CX23)
Pfam (PF01775)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L18a
75XB
(BI)
60S ribosomal protein L5polymer29733764.81UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1,L1a,Ribosomal 5S RNA-binding protein,YL3
76YB
(BJ)
60S ribosomal protein L21-Apolymer16018279.31UniProt (Q02753)
Pfam (PF01157)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
77ZB
(BK)
60S ribosomal protein L33-Apolymer10712177.11UniProt (P05744)
Pfam (PF01247)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L37,RP47,YL37
78AC
(BL)
60S ribosomal protein L22-Apolymer12113711.41UniProt (P05749)
Pfam (PF01776)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L1c,RP4,YL31
79BC
(BM)
60S ribosomal protein L6-Apolymer17620000.61UniProt (Q02326)
Pfam (PF01159)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L17,RP18,YL16
80CC
(BN)
60S ribosomal protein L34-Apolymer12113673.21UniProt (P87262)
Pfam (PF01199)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
81DC
(BO)
60S ribosomal protein L7-Apolymer24427686.31UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)L6,RP11,YL8
82EC
(BP)
60S ribosomal protein L35-Apolymer12013942.61UniProt (P0CX84)
Pfam (PF00831)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
83FC
(BQ)
25S ribosomal RNApolymer33961097493.91REF (831416132)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
84GC
(BR)
5S ribosomal RNApolymer12138951.11GenBank (1039024045)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
85HC
(BS)
5.8S ribosomal RNApolymer15850682.91GenBank (1102645687)Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
86IC
(BT)
Eukaryotic translation initiation factor 5A-1polymer15717222.41UniProt (P23301)
Pfam (PF21485)
Pfam (PF01287)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)eIF-5A-1,Hypusine-containing protein HP2,eIF-4D
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains87
Total formula weight3599383.5
All*Total formula weight3599383.5
*Water molecules are not included.

237423

PDB entries from 2025-06-11

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