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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
1A
(A2)		18S RIBOSOMAL RNApolymer1800577937.51Saccharomyces cerevisiae
2B, CC
(AA, CA)		40S ribosomal protein S0-Apolymer25228051.32UniProt (P32905)
Pfam (PF00318)		Saccharomyces cerevisiae (Baker's yeast)Nucleic acid-binding protein NAB1A
3C, DC
(AB, CB)		40S ribosomal protein S1-Apolymer25528798.52UniProt (P33442)
Pfam (PF01015)		Saccharomyces cerevisiae (Baker's yeast)RP10A
4D, EC
(AC, CC)		40S ribosomal protein S2polymer25427490.82UniProt (P25443)
Pfam (PF00333)
Pfam (PF03719)		Saccharomyces cerevisiae (Baker's yeast)Omnipotent suppressor protein SUP44, RP12, S4, YS5
5E, FC
(AD, CD)		40S ribosomal protein S3polymer24026542.82UniProt (P05750)
Pfam (PF07650)
Pfam (PF00189)		Saccharomyces cerevisiae (Baker's yeast)RP13, YS3
6F, GC
(AE, CE)		40S ribosomal protein S4-Apolymer26129469.32UniProt (P0CX35)
Pfam (PF00900)
Pfam (PF00467)
Pfam (PF16121)
Pfam (PF08071)
Pfam (PF01479)		Saccharomyces cerevisiae (Baker's yeast)RP5, S7, YS6
7G, HC
(AF, CF)		40S ribosomal protein S5polymer22525072.62UniProt (P26783)
Pfam (PF00177)		Saccharomyces cerevisiae (Baker's yeast)RP14, S2, YS8
8H, IC
(AG, CG)		40S ribosomal protein S6-Apolymer23627054.52UniProt (P0CX37)
Pfam (PF01092)		Saccharomyces cerevisiae (Baker's yeast)RP9, S10, YS4
9I, JC
(AH, CH)		40S ribosomal protein S7-Apolymer19021658.22UniProt (P26786)
Pfam (PF01251)		Saccharomyces cerevisiae (Baker's yeast)RP30, RP40
10J, KC
(AI, CI)		40S ribosomal protein S8-Apolymer20022537.82UniProt (P0CX39)
Pfam (PF01201)		Saccharomyces cerevisiae (Baker's yeast)RP19, S14, YS9
11K, LC
(AJ, CJ)		40S ribosomal protein S9-Apolymer19722487.92UniProt (O13516)
Pfam (PF00163)
Pfam (PF01479)		Saccharomyces cerevisiae (Baker's yeast)RP21, S13, YP28, YS11
12L, MC
(AK, CK)		40S ribosomal protein S10-Apolymer10512757.42UniProt (Q08745)
Pfam (PF03501)		Saccharomyces cerevisiae (Baker's yeast)
13M, NC
(AL, CL)		40S ribosomal protein S11-Apolymer15617785.92UniProt (P0CX47)
Pfam (PF16205)
Pfam (PF00366)		Saccharomyces cerevisiae (Baker's yeast)RP41, S18, YS12
14N, OC
(AM, CM)		40S ribosomal protein S12polymer14315488.62UniProt (P48589)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)
15O, PC
(AN, CN)		40S ribosomal protein S13polymer15117059.92UniProt (P05756)
Pfam (PF08069)
Pfam (PF00312)		Saccharomyces cerevisiae (Baker's yeast)S27a, YS15
16P, QC
(AO, CO)		40S ribosomal protein S14-Apolymer13714562.72UniProt (P06367)
Pfam (PF00411)		Saccharomyces cerevisiae (Baker's yeast)RP59A
17Q, RC
(AP, CP)		40S ribosomal protein S15polymer14216031.92UniProt (Q01855)
Pfam (PF00203)		Saccharomyces cerevisiae (Baker's yeast)RIG protein, RP52, S21, YS21
18R, SC
(AQ, CQ)		40S ribosomal protein S16-Apolymer14315877.52UniProt (P0CX51)
Pfam (PF00380)		Saccharomyces cerevisiae (Baker's yeast)RP61R
19S, TC
(AR, CR)		40S ribosomal protein S17-Apolymer13615820.42UniProt (P02407)
Pfam (PF00833)		Saccharomyces cerevisiae (Baker's yeast)RP51A
20T, UC
(AS, CS)		40S ribosomal protein S18-Apolymer14617071.62UniProt (P0CX55)
Pfam (PF00416)		Saccharomyces cerevisiae (Baker's yeast)
21U, VC
(AT, CT)		40S ribosomal protein S19-Apolymer14415942.12UniProt (P07280)
Pfam (PF01090)		Saccharomyces cerevisiae (Baker's yeast)RP55A, S16a, YP45, YS16A
22V, WC
(AU, CU)		40S ribosomal protein S20polymer12113929.02UniProt (P38701)
Pfam (PF00338)		Saccharomyces cerevisiae (Baker's yeast)
23W, XC
(AV, CV)		40S ribosomal protein S21-Apolymer879758.82UniProt (P0C0V8)
Pfam (PF01249)		Saccharomyces cerevisiae (Baker's yeast)S26, YS25
24X, YC
(AW, CW)		40S ribosomal protein S22-Apolymer13014650.12UniProt (P0C0W1)
Pfam (PF00410)		Saccharomyces cerevisiae (Baker's yeast)RP50, S24, YP58, YS22
25Y, ZC
(AX, CX)		40S ribosomal protein S23-Apolymer14516073.92UniProt (P0CX29)
Pfam (PF00164)		Saccharomyces cerevisiae (Baker's yeast)RP37, S28, YS14
26AD, Z
(AY, CY)		40S ribosomal protein S24-Apolymer13515362.82UniProt (P0CX31)
Pfam (PF01282)		Saccharomyces cerevisiae (Baker's yeast)RP50
27AA, BD
(AZ, CZ)		40S ribosomal protein S25-Apolymer10812067.32UniProt (Q3E792)
Pfam (PF03297)		Saccharomyces cerevisiae (Baker's yeast)RP45, S31, YS23
28BA, CD
(Aa, Ca)		40S ribosomal protein S26-Apolymer11913538.92UniProt (P39938)
Pfam (PF01283)		Saccharomyces cerevisiae (Baker's yeast)
29CA, DD
(Ab, Cb)		40S ribosomal protein S27-Apolymer828893.42UniProt (P35997)
Pfam (PF01667)		Saccharomyces cerevisiae (Baker's yeast)RP61, YS20
30DA, ED
(Ac, Cc)		40S ribosomal protein S28-Apolymer677605.82UniProt (Q3E7X9)
Pfam (PF01200)		Saccharomyces cerevisiae (Baker's yeast)S33, YS27
31EA, FD
(Ad, Cd)		40S ribosomal protein S29-Apolymer566675.72UniProt (P41057)
Pfam (PF00253)		Saccharomyces cerevisiae (Baker's yeast)S36, YS29
32FA, GD
(Ae, Ce)		40S ribosomal protein S30-Apolymer637137.52UniProt (P0CX33)
Pfam (PF04758)		Saccharomyces cerevisiae (Baker's yeast)
33GA, HD
(Af, Cf)		40S ribosomal protein S31polymer15216383.02UniProt (P05759)
Pfam (PF00240)
Pfam (PF01599)		Saccharomyces cerevisiae (Baker's yeast)40S ribosomal protein S31, CEP76, S37, YS24
34HA, ID
(Ag, Cg)		Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1)polymer31934841.22UniProt (P38011)
Pfam (PF00400)		Saccharomyces cerevisiae (Baker's yeast)Receptor for activated C kinase, Receptor of activated protein kinase C 1, RACK1
35IA
(Ah)		Suppressor protein STM1polymer27329052.41UniProt (P39015)
Pfam (PF09598)		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
36JA, KD
(A1, A5)		25S rRNApolymer33961097493.92Saccharomyces cerevisiae
37KA, LD
(A3, A7)		5S rRNApolymer12138951.12Saccharomyces cerevisiae
38LA, MD
(A4, A8)		5.8S rRNApolymer15850682.92Saccharomyces cerevisiae
39MA, ND
(BA, DA)		60S ribosomal protein L2-Apolymer25427463.62UniProt (P0CX45)
Pfam (PF00181)
Pfam (PF03947)		Saccharomyces cerevisiae (Baker's yeast)L5, RP8, YL6
40NA, OD
(BB, DB)		60S ribosomal protein L3polymer38743850.82UniProt (P14126)
Pfam (PF00297)		Saccharomyces cerevisiae (Baker's yeast)Maintenance of killer protein 8, RP1, Trichodermin resistance protein, YL1
41OA, PD
(BC, DC)		60S ribosomal protein L4-Apolymer36239159.12UniProt (P10664)
Pfam (PF00573)
Pfam (PF14374)		Saccharomyces cerevisiae (Baker's yeast)L2, RP2, YL2
42PA, QD
(BD, DD)		60S ribosomal protein L5polymer29733764.82UniProt (P26321)
Pfam (PF17144)
Pfam (PF14204)		Saccharomyces cerevisiae (Baker's yeast)L1, L1a, Ribosomal 5S RNA-binding protein, YL3
43QA, RD
(BE, DE)		60S ribosomal protein L6-Apolymer17620000.62UniProt (Q02326)
Pfam (PF01159)		Saccharomyces cerevisiae (Baker's yeast)L17, RP18, YL16
44RA, SD
(BF, DF)		60S ribosomal protein L7-Apolymer24427686.32UniProt (P05737)
Pfam (PF08079)
Pfam (PF00327)		Saccharomyces cerevisiae (Baker's yeast)L6, RP11, YL8
45SA, TD
(BG, DG)		60S ribosomal protein L8-Apolymer25628175.82UniProt (P17076)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)L4, L4-2, L7a-1, Maintenance of killer protein 7, RP6, YL5
46TA, UD
(BH, DH)		60S ribosomal protein L9-Apolymer19121605.12UniProt (P05738)
Pfam (PF00347)		Saccharomyces cerevisiae (Baker's yeast)L8, RP24, YL11
47UA, VD
(BI, DI)		60S ribosomal protein L10polymer22125410.52UniProt (P41805)
Pfam (PF00252)		Saccharomyces cerevisiae (Baker's yeast)L9, Ubiquinol-cytochrome C reductase complex subunit VI-requiring protein
48VA, WD
(BJ, DJ)		60S ribosomal protein L11-Apolymer17419755.72UniProt (P0C0W9)
Pfam (PF00281)
Pfam (PF00673)		Saccharomyces cerevisiae (Baker's yeast)L16, RP39, YL22
49WA, YD
(BL, DL)		60S ribosomal protein L13-Apolymer19922604.22UniProt (Q12690)
Pfam (PF01294)		Saccharomyces cerevisiae (Baker's yeast)
50XA, ZD
(BM, DM)		60S ribosomal protein L14-Apolymer13815195.12UniProt (P36105)
Pfam (PF00467)
Pfam (PF01929)		Saccharomyces cerevisiae (Baker's yeast)
51AE, YA
(BN, DN)		60S ribosomal protein L15-Apolymer20424482.42UniProt (P05748)
Pfam (PF00827)		Saccharomyces cerevisiae (Baker's yeast)L13, RP15R, YL10, YP18
52BE, ZA
(BO, DO)		60S ribosomal protein L16-A, 60S ribosomal protein L16-Bpolymer19922247.22UniProt (P26784)
Pfam (PF00572)		Saccharomyces cerevisiae (Baker's yeast)L13a, L21, RP22, YL15
53AB, CE
(BP, DP)		60S ribosomal protein L17-Apolymer18420589.52UniProt (P05740)
Pfam (PF00237)		Saccharomyces cerevisiae (Baker's yeast)L20A, YL17
54BB, DE
(BQ, DQ)		60S ribosomal protein L18-Apolymer18620609.32UniProt (P0CX49)
Pfam (PF17135)		Saccharomyces cerevisiae (Baker's yeast)RP28
55CB, EE
(BR, DR)		60S ribosomal protein L19-Apolymer18921762.32UniProt (P0CX82)
Pfam (PF01280)		Saccharomyces cerevisiae (Baker's yeast)L23, RP15L, RP33, YL14
56DB, FE
(BS, DS)		60S ribosomal protein L20-Apolymer17220478.92UniProt (P0CX23)
Pfam (PF01775)		Saccharomyces cerevisiae (Baker's yeast)L18a
57EB, GE
(BT, DT)		60S ribosomal protein L21-Apolymer16018279.32UniProt (Q02753)
Pfam (PF01157)		Saccharomyces cerevisiae (Baker's yeast)
58FB, HE
(BU, DU)		60S ribosomal protein L22-Apolymer12113711.42UniProt (P05749)
Pfam (PF01776)		Saccharomyces cerevisiae (Baker's yeast)L1c, RP4, YL31
59GB, IE
(BV, DV)		60S ribosomal protein L23-Apolymer13714494.02UniProt (P0CX41)
Pfam (PF00238)		Saccharomyces cerevisiae (Baker's yeast)L17a, YL32
60HB, JE
(BW, DW)		60S ribosomal protein L24-Apolymer15517661.72UniProt (P04449)
Pfam (PF01246)		Saccharomyces cerevisiae (Baker's yeast)L30, RP29, YL21
61IB, KE
(BX, DX)		60S ribosomal protein L25polymer14215787.62UniProt (P04456)
Pfam (PF03939)
Pfam (PF00276)		Saccharomyces cerevisiae (Baker's yeast)RP16L, YL25, YP42'
62JB, LE
(BY, DY)		60S ribosomal protein L26-Apolymer12714265.82UniProt (P05743)
Pfam (PF16906)
Pfam (PF00467)		Saccharomyces cerevisiae (Baker's yeast)L33, YL33
63KB, ME
(BZ, DZ)		60S ribosomal protein L27-Apolymer13615568.42UniProt (P0C2H6)
Pfam (PF01777)		Saccharomyces cerevisiae (Baker's yeast)
64LB, NE
(Ba, Da)		60S ribosomal protein L28polymer14916761.72UniProt (P02406)
Pfam (PF00828)		Saccharomyces cerevisiae (Baker's yeast)L27a, L29, RP44, RP62, YL24
65MB, OE
(Bb, Db)		60S ribosomal protein L29polymer596691.92UniProt (P05747)
Pfam (PF01779)		Saccharomyces cerevisiae (Baker's yeast)YL43
66NB, PE
(Bc, Dc)		60S ribosomal protein L30polymer10511430.42UniProt (P14120)
Pfam (PF01248)		Saccharomyces cerevisiae (Baker's yeast)L32, RP73, YL38
67OB, QE
(Bd, Dd)		60S ribosomal protein L31-Apolymer11312980.22UniProt (P0C2H8)
Pfam (PF01198)		Saccharomyces cerevisiae (Baker's yeast)L34, YL28
68PB, RE
(Be, De)		60S ribosomal protein L32polymer13014809.42UniProt (P38061)
Pfam (PF01655)		Saccharomyces cerevisiae (Baker's yeast)
69QB, SE
(Bf, Df)		60S ribosomal protein L33-Apolymer10712177.12UniProt (P05744)
Pfam (PF01247)		Saccharomyces cerevisiae (Baker's yeast)L37, RP47, YL37
70RB, TE
(Bg, Dg)		60S ribosomal protein L34-Apolymer12113673.22UniProt (P87262)
Pfam (PF01199)		Saccharomyces cerevisiae (Baker's yeast)
71SB, UE
(Bh, Dh)		60S ribosomal protein L35-Apolymer12013942.62UniProt (P0CX84)
Pfam (PF00831)		Saccharomyces cerevisiae (Baker's yeast)
72TB, VE
(Bi, Di)		60S ribosomal protein L36-Apolymer10011151.32UniProt (P05745)
Pfam (PF01158)		Saccharomyces cerevisiae (Baker's yeast)L39, YL39
73UB, WE
(Bj, Dj)		60S ribosomal protein L37-Apolymer889877.42UniProt (P49166)
Pfam (PF01907)		Saccharomyces cerevisiae (Baker's yeast)L43, YL35, YP55
74VB, XE
(Bk, Dk)		60S ribosomal protein L38polymer788845.62UniProt (P49167)
Pfam (PF01781)		Saccharomyces cerevisiae (Baker's yeast)
75WB, YE
(Bl, Dl)		60S ribosomal protein L39polymer516358.62UniProt (P04650)
Pfam (PF00832)		Saccharomyces cerevisiae (Baker's yeast)L46, YL40
76XB, ZE
(Bm, Dm)		60S ribosomal protein L40polymer12814583.12UniProt (P0CH08)
Pfam (PF00240)
Pfam (PF01020)		Saccharomyces cerevisiae (Baker's yeast)60S ribosomal protein L40, CEP52
77AF, YB
(Bn, Dn)		60S ribosomal protein L41-Apolymer253354.22UniProt (P0CX86)
Pfam (PF05162)		Saccharomyces cerevisiae (Baker's yeast)L47, YL41
78BF, ZB
(Bo, Do)		60S ribosomal protein L42-Apolymer10612246.72UniProt (P0CX27)
Pfam (PF00935)		Saccharomyces cerevisiae (Baker's yeast)L41, YL27, YP44
79AC, CF
(Bp, Dp)		60S ribosomal protein L43-Apolymer9210113.02UniProt (P0CX25)
Pfam (PF01780)		Saccharomyces cerevisiae (Baker's yeast)L37a, YL35
80BC
(A6)		18S rRNApolymer1800576517.41Saccharomyces cerevisiae
81JD
(Ch)		Suppressor 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
82XD
(DK)		Ribosomal protein L12polymer15513209.31Saccharomyces cerevisiae
83DF
(Dq)		60S acidic ribosomal protein P0polymer31233289.81UniProt (P05317)
Pfam (PF00466)
Pfam (PF17777)
Pfam (PF00428)		Saccharomyces cerevisiae (Baker's yeast)A0, L10E
84EF
(Dr)		Ribosomal protein P1 alphapolymer474017.91Saccharomyces cerevisiae
85FF
(Ds)		Ribosomal protein P2 betapolymer463932.81Saccharomyces cerevisiae
86AAA, AAC, AAD, ABA, ABD...
(A1, A6, A5, A7, A2...)		osmium (III) hexamminenon-polymer286.41345Chemie (OHX)
87AAB, AAE, ABB, ABC, ABE...
(A1, A5, A6, A7, A8...)		MAGNESIUM IONnon-polymer24.32205Chemie (MG)
88ALC, AME, BU, DU, EME...
(Cf, Dm, Ad, Af, Do...)		ZINC IONnon-polymer65.416Chemie (ZN)
89KME, LME
(CI, DB)		waterwater18.02Chemie (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.

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PDB entries from 2025-06-18

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