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SummaryStructural detailsExperimental detailsFunctional detailsSequence NeighborHistoryDownloads

4V88

The structure of the eukaryotic ribosome at 3.0 A resolution.

This is a non-PDB format compatible entry.
Entity
Entity IDChain IDDescriptionTypeChain lengthFormula weightNumber of moleculesDB Name (Accession)Biological sourceDescriptive keywords
1A218S RIBOSOMAL RNApolymer1800577937.51Saccharomyces cerevisiae
2AA, CA40S ribosomal protein S0-Apolymer25228051.32UniProt (P32905)
Pfam (PF00318)
In PDB		Saccharomyces cerevisiae (Baker's yeast)Nucleic acid-binding protein NAB1A
3AB, CB40S ribosomal protein S1-Apolymer25528798.52UniProt (P33442)
Pfam (PF01015)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP10A
4AC, CC40S ribosomal protein S2polymer25427490.82UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)
In PDB		Saccharomyces cerevisiae (Baker's yeast)Omnipotent suppressor protein SUP44, RP12, S4, YS5
5AD, CD40S ribosomal protein S3polymer24026542.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP13, YS3
6AE, CE40S ribosomal protein S4-Apolymer26129469.32UniProt (P0CX35)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Pfam (PF08071)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP5, S7, YS6
7AF, CF40S ribosomal protein S5polymer22525072.62UniProt (P26783)
Pfam (PF00177)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP14, S2, YS8
8AG, CG40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP9, S10, YS4
9AH, CH40S ribosomal protein S7-Apolymer19021658.22UniProt (P26786)
Pfam (PF01251)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP30, RP40
10AI, CI40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP19, S14, YS9
11AJ, CJ40S ribosomal protein S9-Apolymer19722487.92UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP21, S13, YP28, YS11
12AK, CK40S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
13AL, CL40S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP41, S18, YS12
14AM, CM40S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
15AN, CN40S ribosomal protein S13polymer15117059.92UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)
In PDB		Saccharomyces cerevisiae (Baker's yeast)S27a, YS15
16AO, CO40S ribosomal protein S14-Apolymer13714562.72UniProt (P06367)
Pfam (PF00411)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP59A
17AP, CP40S ribosomal protein S15polymer14216031.92UniProt (Q01855)
Pfam (PF00203)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RIG protein, RP52, S21, YS21
18AQ, CQ40S ribosomal protein S16-Apolymer14315877.52UniProt (P0CX51)
Pfam (PF00380)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP61R
19AR, CR40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP51A
20AS, CS40S ribosomal protein S18-Apolymer14617071.62UniProt (P0CX55)
Pfam (PF00416)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
21AT, CT40S ribosomal protein S19-Apolymer14415942.12UniProt (P07280)
Pfam (PF01090)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP55A, S16a, YP45, YS16A
22AU, CU40S ribosomal protein S20polymer12113929.02UniProt (P38701)
Pfam (PF00338)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
23AV, CV40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)
In PDB		Saccharomyces cerevisiae (Baker's yeast)S26, YS25
24AW, CW40S ribosomal protein S22-Apolymer13014650.12UniProt (P0C0W1)
Pfam (PF00410)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP50, S24, YP58, YS22
25AX, CX40S ribosomal protein S23-Apolymer14516073.92UniProt (P0CX29)
Pfam (PF00164)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP37, S28, YS14
26AY, CY40S ribosomal protein S24-Apolymer13515362.82UniProt (P0CX31)
Pfam (PF01282)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP50
27AZ, CZ40S ribosomal protein S25-Apolymer10812067.32UniProt (Q3E792)
Pfam (PF03297)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP45, S31, YS23
28Aa, Ca40S ribosomal protein S26-Apolymer11913538.92UniProt (P39938)
Pfam (PF01283)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
29Ab, Cb40S ribosomal protein S27-Apolymer828893.42UniProt (P35997)
Pfam (PF01667)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP61, YS20
30Ac, Cc40S ribosomal protein S28-Apolymer677605.82UniProt (Q3E7X9)
Pfam (PF01200)
In PDB		Saccharomyces cerevisiae (Baker's yeast)S33, YS27
31Ad, Cd40S ribosomal protein S29-Apolymer566675.72UniProt (P41057)
Pfam (PF00253)
In PDB		Saccharomyces cerevisiae (Baker's yeast)S36, YS29
32Ae, Ce40S ribosomal protein S30-Apolymer637137.52UniProt (P0CX33)
Pfam (PF04758)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
33Af, Cf40S ribosomal protein S31polymer15216383.02UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)
In PDB		Saccharomyces cerevisiae (Baker's yeast)40S ribosomal protein S31, CEP76, S37, YS24
34Ag, CgGuanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1)polymer31934841.22UniProt (P38011)
Pfam (PF00400)
In PDB		Saccharomyces cerevisiae (Baker's yeast)Receptor for activated C kinase, Receptor of activated protein kinase C 1, RACK1
35AhSuppressor protein STM1polymer27329052.41UniProt (P39015)
Pfam (PF09598)
In PDB		Saccharomyces cerevisiae (Baker's yeast)3BP1, GU4 nucleic-binding protein 2, G4p2 protein, POP2 multicopy suppressor protein 4, Ribosomal subunits association factor, AF, TOM1 suppressor protein 1, Triplex-binding protein 1
36A1, A525S rRNApolymer33961097493.92Saccharomyces cerevisiae
37A3, A75S rRNApolymer12138951.12Saccharomyces cerevisiae
38A4, A85.8S rRNApolymer15850682.92Saccharomyces cerevisiae
39BA, DA60S ribosomal protein L2-Apolymer25427463.62UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L5, RP8, YL6
40BB, DB60S ribosomal protein L3polymer38743850.82UniProt (P14126)
Pfam (PF00297)
In PDB		Saccharomyces cerevisiae (Baker's yeast)Maintenance of killer protein 8, RP1, Trichodermin resistance protein, YL1
41BC, DC60S ribosomal protein L4-Apolymer36239159.12UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L2, RP2, YL2
42BD, DD60S ribosomal protein L5polymer29733764.82UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L1, L1a, Ribosomal 5S RNA-binding protein, YL3
43BE, DE60S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L17, RP18, YL16
44BF, DF60S ribosomal protein L7-Apolymer24427686.32UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L6, RP11, YL8
45BG, DG60S ribosomal protein L8-Apolymer25628175.82UniProt (P17076)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L4, L4-2, L7a-1, Maintenance of killer protein 7, RP6, YL5
46BH, DH60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L8, RP24, YL11
47BI, DI60S ribosomal protein L10polymer22125410.52UniProt (P41805)
Pfam (PF00252)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L9, Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48BJ, DJ60S ribosomal protein L11-Apolymer17419755.72UniProt (P0C0W9)
Pfam (PF00673)
Pfam (PF00281)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L16, RP39, YL22
49BL, DL60S ribosomal protein L13-Apolymer19922604.22UniProt (Q12690)
Pfam (PF01294)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
50BM, DM60S ribosomal protein L14-Apolymer13815195.12UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
51BN, DN60S ribosomal protein L15-Apolymer20424482.42UniProt (P05748)
Pfam (PF00827)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L13, RP15R, YL10, YP18
52BO, DO60S ribosomal protein L16-A, 60S ribosomal protein L16-Bpolymer19922247.22UniProt (P26784)
Pfam (PF00572)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L13a, L21, RP22, YL15
53BP, DP60S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L20A, YL17
54BQ, DQ60S ribosomal protein L18-Apolymer18620609.32UniProt (P0CX49)
Pfam (PF17135)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP28
55BR, DR60S ribosomal protein L19-Apolymer18921762.32UniProt (P0CX82)
Pfam (PF01280)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L23, RP15L, RP33, YL14
56BS, DS60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L18a
57BT, DT60S ribosomal protein L21-Apolymer16018279.32UniProt (Q02753)
Pfam (PF01157)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
58BU, DU60S ribosomal protein L22-Apolymer12113711.42UniProt (P05749)
Pfam (PF01776)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L1c, RP4, YL31
59BV, DV60S ribosomal protein L23-Apolymer13714494.02UniProt (P0CX41)
Pfam (PF00238)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L17a, YL32
60BW, DW60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L30, RP29, YL21
61BX, DX60S ribosomal protein L25polymer14215787.62UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)
In PDB		Saccharomyces cerevisiae (Baker's yeast)RP16L, YL25, YP42'
62BY, DY60S ribosomal protein L26-Apolymer12714265.82UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L33, YL33
63BZ, DZ60S ribosomal protein L27-Apolymer13615568.42UniProt (P0C2H6)
Pfam (PF01777)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
64Ba, Da60S ribosomal protein L28polymer14916761.72UniProt (P02406)
Pfam (PF00828)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L27a, L29, RP44, RP62, YL24
65Bb, Db60S ribosomal protein L29polymer596691.92UniProt (P05747)
Pfam (PF01779)
In PDB		Saccharomyces cerevisiae (Baker's yeast)YL43
66Bc, Dc60S ribosomal protein L30polymer10511430.42UniProt (P14120)
Pfam (PF01248)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L32, RP73, YL38
67Bd, Dd60S ribosomal protein L31-Apolymer11312980.22UniProt (P0C2H8)
Pfam (PF01198)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L34, YL28
68Be, De60S ribosomal protein L32polymer13014809.42UniProt (P38061)
Pfam (PF01655)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
69Bf, Df60S ribosomal protein L33-Apolymer10712177.12UniProt (P05744)
Pfam (PF01247)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L37, RP47, YL37
70Bg, Dg60S ribosomal protein L34-Apolymer12113673.22UniProt (P87262)
UniProt (by SIFTS) (P0CX25)
Pfam (PF01199)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
71Bh, Dh60S ribosomal protein L35-Apolymer12013942.62UniProt (P0CX84)
Pfam (PF00831)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
72Bi, Di60S ribosomal protein L36-Apolymer10011151.32UniProt (P05745)
Pfam (PF01158)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L39, YL39
73Bj, Dj60S ribosomal protein L37-Apolymer889877.42UniProt (P49166)
Pfam (PF01907)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L43, YL35, YP55
74Bk, Dk60S ribosomal protein L38polymer788845.62UniProt (P49167)
Pfam (PF01781)
In PDB		Saccharomyces cerevisiae (Baker's yeast)
75Bl, Dl60S ribosomal protein L39polymer516358.62UniProt (P04650)
Pfam (PF00832)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L46, YL40
76Bm, Dm60S ribosomal protein L40polymer12814583.12UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)
In PDB		Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L40, CEP52
77Bn, Dn60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L47, YL41
78Bo, Do60S ribosomal protein L42-Apolymer10612246.72UniProt (P0CX27)
Pfam (PF00935)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L41, YL27, YP44
79Bp, Dp60S ribosomal protein L43-Apolymer9210113.02UniProt (P0CX25)
Pfam (PF01780)
In PDB		Saccharomyces cerevisiae (Baker's yeast)L37a, YL35
80A618S rRNApolymer1800576517.41Saccharomyces cerevisiae
81ChSuppressor protein STM1polymer27329153.61Saccharomyces cerevisiae (Baker's yeast)3BP1, GU4 nucleic-binding protein 2, G4p2 protein, POP2 multicopy suppressor protein 4, Ribosomal subunits association factor, AF, TOM1 suppressor protein 1, Triplex-binding protein 1
82DKRibosomal protein L12polymer15513209.31Saccharomyces cerevisiae
83Dq60S acidic ribosomal protein P0polymer31233289.81UniProt (P05317)
Pfam (PF00428)
Pfam (PF00466)
Pfam (PF17777)
In PDB		Saccharomyces cerevisiae (Baker's yeast)A0, L10E
84DrRibosomal protein P1 alphapolymer474017.91Saccharomyces cerevisiae
85DsRibosomal protein P2 betapolymer463932.81Saccharomyces cerevisiae
86A1, A6, A5, A7, A2...osmium (III) hexamminenon-polymer286.41345Chemie (OHX)
87A1, A5, A6, A7, A8...MAGNESIUM IONnon-polymer24.32205Chemie (MG)
88Cf, Dm, Ad, Af, Do...ZINC IONnon-polymer65.416Chemie (ZN)
89waterwater18.02Chemie (HOH)
Sequence modifications
Af, Cf: 1 - 152 (UniProt: P05759)
PDBExternal DatabaseDetails
Unk 82Lys 82SEE REMARK 999
Unk 83Lys 83SEE REMARK 999
Unk 84Val 84SEE REMARK 999
Unk 85Tyr 85SEE REMARK 999
Unk 86Thr 86SEE REMARK 999
Unk 87Thr 87SEE REMARK 999
Unk 88Pro 88SEE REMARK 999
Unk 89Lys 89SEE REMARK 999
Unk 90Lys 90SEE REMARK 999
Unk 91Ile 91SEE REMARK 999
Unk 92Lys 92SEE REMARK 999
Unk 93His 93SEE REMARK 999
Unk 94Lys 94SEE REMARK 999
Unk 95His 95SEE REMARK 999
Unk 96Lys 96SEE REMARK 999
Unk 97Lys 97SEE REMARK 999
Unk 98Val 98SEE REMARK 999
Unk 99Lys 99SEE REMARK 999
Unk 100Leu 100SEE REMARK 999
Unk 101Ala 101SEE REMARK 999
Ah: 1 - 273 (UniProt: P39015)
PDBExternal DatabaseDetails
Unk 9Gly 9SEE REMARK 999
Unk 10Asn 10SEE REMARK 999
Unk 11Asp 11SEE REMARK 999
Unk 12Val 12SEE REMARK 999
Unk 13Glu 13SEE REMARK 999
Unk 14Asp 14SEE REMARK 999
Unk 15Ala 15SEE REMARK 999
Unk 16Asp 16SEE REMARK 999
Unk 17Val 17SEE REMARK 999
Unk 18Val 18SEE REMARK 999
Unk 19Val 19SEE REMARK 999
Unk 20Leu 20SEE REMARK 999
Unk 151Leu 151SEE REMARK 999
Unk 152Gln 152SEE REMARK 999
Unk 153Asp 153SEE REMARK 999
Unk 154Tyr 154SEE REMARK 999
Unk 155Leu 155SEE REMARK 999
Unk 156Asn 156SEE REMARK 999
Unk 157Gln 157SEE REMARK 999
Unk 158Gln 158SEE REMARK 999
Unk 159Ala 159SEE REMARK 999
Unk 160Asn 160SEE REMARK 999
Unk 161Asn 161SEE REMARK 999
Unk 162Gln 162SEE REMARK 999
Unk 163Phe 163SEE REMARK 999
Unk 164Asn 164SEE REMARK 999
Unk 165Lys 165SEE REMARK 999
Unk 166Val 166SEE REMARK 999
Unk 167Pro 167SEE REMARK 999
Unk 168Glu 168SEE REMARK 999
Unk 169Ala 169SEE REMARK 999
Unk 170Lys 170SEE REMARK 999
Unk 171Lys 171SEE REMARK 999
Unk 172Val 172SEE REMARK 999
Unk 173Glu 173SEE REMARK 999
Unk 174Leu 174SEE REMARK 999
Unk 175Asp 175SEE REMARK 999
Unk 176Ala 176SEE REMARK 999
Dq: 1 - 312 (UniProt: P05317)
PDBExternal DatabaseDetails
Unk 199Ser 199SEE REMARK 999
Unk 200Ser 200SEE REMARK 999
Unk 201Ile 201SEE REMARK 999
Unk 202Leu 202SEE REMARK 999
Unk 203Asp 203SEE REMARK 999
Unk 204Ile 204SEE REMARK 999
Unk 205Thr 205SEE REMARK 999
Unk 206Asp 206SEE REMARK 999
Unk 207Glu 207SEE REMARK 999
Unk 208Glu 208SEE REMARK 999
Unk 209Leu 209SEE REMARK 999
Unk 210Val 210SEE REMARK 999
Unk 211Ser 211SEE REMARK 999
Unk 212His 212SEE REMARK 999
Unk 213Phe 213SEE REMARK 999
Unk 214Val 214SEE REMARK 999
Unk 215Ser 215SEE REMARK 999
Unk 216Ala 216SEE REMARK 999
Unk 217Val 217SEE REMARK 999
Unk 218Ser 218SEE REMARK 999
Unk 219Thr 219SEE REMARK 999
Unk 220Ile 220SEE REMARK 999
Unk 221Ala 221SEE REMARK 999
Sequence viewer
Contents of the asymmetric unit
PolymersNumber of chains162
Total formula weight6317536.1
Non-Polymers*Number of molecules3566
Total formula weight439800.0
All*Total formula weight6757336.1
*Water molecules are not included.

222415

PDB entries from 2024-07-10

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