4V88

The structure of the eukaryotic ribosome at 3.0 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181

Literature

Macromolecules
Sequence Display for 4V88

Classification: RIBOSOME

Total Structure Weight: 6757336.00


Macromolecule Entities
Molecule Chains Length Organism Details
40S ribosomal protein S0-A AA, CA 252 Saccharomyces cerevisiae Gene Name(s): RPS0A NAB1 Gene View NAB1A YST1 YGR214W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S1-A AB, CB 255 Saccharomyces cerevisiae Gene Name(s): RPS1A PLC1 RPS10A YLR441C L9753.9
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S2 AC, CC 254 Saccharomyces cerevisiae Gene Name(s): RPS2 Gene View RPS4 SUP38 SUP44 YGL123W G2893
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S3 AD, CD 240 Saccharomyces cerevisiae Gene Name(s): RPS3 Gene View SUF14 YNL178W N1653
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S4-A AE, CE 261 Saccharomyces cerevisiae Gene Name(s): RPS4A RPS7B YJR145C J2186
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S5 AF, CF 225 Saccharomyces cerevisiae Gene Name(s): RPS5 Gene View RPS2 Gene View YJR123W J2045
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S6-A AG, CG 236 Saccharomyces cerevisiae Gene Name(s): RPS6A RPS101 RPS10B YPL090C LPG18C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S7-A AH, CH 190 Saccharomyces cerevisiae Gene Name(s): RPS7A RPS30 YOR096W YOR3177W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S8-A AI, CI 200 Saccharomyces cerevisiae Gene Name(s): RPS8A RPS14A YBL072C YBL06.05 YBL0613
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S9-A AJ, CJ 197 Saccharomyces cerevisiae Gene Name(s): RPS9A RPS13A YS11A YPL081W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S10-A AK, CK 105 Saccharomyces cerevisiae Gene Name(s): RPS10A YOR293W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S11-A AL, CL 156 Saccharomyces cerevisiae Gene Name(s): RPS11A RPS18A YDR025W YD9813.03
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S12 AM, CM 143 Saccharomyces cerevisiae Gene Name(s): RPS12 Gene View YOR369C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S13 AN, CN 151 Saccharomyces cerevisiae Gene Name(s): RPS13 Gene View RPS13C YDR064W D4252 YD9609.18
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S14-A AO, CO 137 Saccharomyces cerevisiae Gene Name(s): RPS14A CRY1 Gene View RPL59 YCR031C YCR31C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S15 AP, CP 142 Saccharomyces cerevisiae Gene Name(s): RPS15 Gene View RPS21 Gene View YOL040C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S16-A AQ, CQ 143 Saccharomyces cerevisiae EC#: 1.1.1.189 IUBMB
Gene Name(s): RPS16A RP61R YMR143W YM9375.12
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S17-A AR, CR 136 Saccharomyces cerevisiae Gene Name(s): RPS17A RP51A YML024W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S18-A AS, CS 146 Saccharomyces cerevisiae Gene Name(s): RPS18A YDR450W D9461.35
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S19-A AT, CT 144 Saccharomyces cerevisiae Gene Name(s): RPS19A RP55A RPS16AA YOL121C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S20 AU, CU 121 Saccharomyces cerevisiae Gene Name(s): RPS20 Gene View URP2 YHL015W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S21-A AV, CV 87 Saccharomyces cerevisiae Gene Name(s): RPS21A RPS25 Gene View RPS25A RPS26A YKR057W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S22-A AW, CW 130 Saccharomyces cerevisiae Gene Name(s): RPS22A RPS24 Gene View RPS24A YJL190C J0355
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S23-A AX, CX 145 Saccharomyces cerevisiae Gene Name(s): RPS23A RPS28A YGR118W G6178
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S24-A AY, CY 135 Saccharomyces cerevisiae Gene Name(s): RPS24A RPS24EA YER074W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S25-A AZ, CZ 108 Saccharomyces cerevisiae Gene Name(s): RPS25A RPS31A YGR027C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S26-A Aa, Ca 119 Saccharomyces cerevisiae Gene Name(s): RPS26A RPS26 Gene View YGL189C G1355
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S27-A Ab, Cb 82 Saccharomyces cerevisiae Gene Name(s): RPS27A Gene View YKL156W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S28-A Ac, Cc 67 Saccharomyces cerevisiae Gene Name(s): RPS28A RPS33 RPS33A YOR167C O3600
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S29-A Ad, Cd 56 Saccharomyces cerevisiae Gene Name(s): RPS29A RPS36A YS29A YLR388W L8084.11
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S30-A Ae, Ce 63 Saccharomyces cerevisiae Gene Name(s): RPS30A YLR287C-A L8003.23 YLR287BC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
40S ribosomal protein S31 Af, Cf 152 Saccharomyces cerevisiae Mutation: K82X, K83X, V84X, Y85X, T86X, T87X, P88X, K89X, K90X, I91X, K92X, H93X, K94X, H95X, K96X, K97X, V98X, K99X, L100X, A101X
Gene Name(s): RPS31 RPS37 UBI3 YLR167W L9470.14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1) Ag, Cg 319 Saccharomyces cerevisiae Gene Name(s): ASC1 CPC2 YMR116C YM9718.15C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Suppressor protein STM1 Ah 273 Saccharomyces cerevisiae Mutation: G9X, N10X, D11X, V12X, E13X, D14X, A15X, D16X, V17X, V18X, V19X, L20X, L151X, Q152X, D153X, Y154X, L155X, N156X, Q157X, Q158X, A159X, N160X, N161X, Q162X, F163X, N164X, K165X, V166X, P167X, E168X, A169X, K170X, K171X, V172X, E173X, L174X, D175X, A176X
Gene Name(s): STM1 MPT4 STO1 YLR150W L9634.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L2-A BA, DA 254 Saccharomyces cerevisiae Gene Name(s): RPL2A RPL5B YFR031C-A YFR031BC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L3 BB, DB 387 Saccharomyces cerevisiae Gene Name(s): RPL3 Gene View MAK8 TCM1 YOR063W YOR29-14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L4-A BC, DC 362 Saccharomyces cerevisiae Gene Name(s): RPL4A RPL2 RPL2A YBR031W YBR0315
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L5 BD, DD 297 Saccharomyces cerevisiae Gene Name(s): RPL5 Gene View RPL1 RPL1A YPL131W LPI14W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L6-A BE, DE 176 Saccharomyces cerevisiae Gene Name(s): RPL6A RPL17A YL16A YML073C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L7-A BF, DF 244 Saccharomyces cerevisiae Gene Name(s): RPL7A Gene View RPL6A RPL8A YL8A YGL076C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L8-A BG, DG 256 Saccharomyces cerevisiae Gene Name(s): RPL8A MAK7 RPL4A YHL033C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L9-A BH, DH 191 Saccharomyces cerevisiae Gene Name(s): RPL9A RPL8A RPL9 Gene View YGL147C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L10 BI, DI 221 Saccharomyces cerevisiae Gene Name(s): RPL10 Gene View GRC5 QSR1 YLR075W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L11-A BJ, DJ 174 Saccharomyces cerevisiae Gene Name(s): RPL11A RP39A RPL16A YPR102C P8283.14
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L13-A BL, DL 199 Saccharomyces cerevisiae Gene Name(s): RPL13A Gene View YDL082W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L14-A BM, DM 138 Saccharomyces cerevisiae Gene Name(s): RPL14A YKL006W YKL153
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L15-A BN, DN 204 Saccharomyces cerevisiae Gene Name(s): RPL15A RPL10A Gene View RPL13A Gene View YL10A YLR029C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L16-A, 60S ribosomal protein L16-B BO, DO 199 Saccharomyces cerevisiae Gene Name(s): RPL16A RPL13 Gene View RPL21A YIL133C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L17-A BP, DP 184 Saccharomyces cerevisiae Gene Name(s): RPL17A RPL17 Gene View RPL20A YKL180W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L18-A BQ, DQ 186 Saccharomyces cerevisiae Gene Name(s): RPL18A Gene View RP28A YOL120C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L19-A BR, DR 189 Saccharomyces cerevisiae Gene Name(s): RPL19A RPL23A Gene View YL14A YBR084C-A YBR084BC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L20-A BS, DS 172 Saccharomyces cerevisiae Gene Name(s): RPL20A RPL18A Gene View RPL18A2 YMR242C YM9408.04C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L21-A BT, DT 160 Saccharomyces cerevisiae Gene Name(s): RPL21A URP1 YBR191W YBR1401
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L22-A BU, DU 121 Saccharomyces cerevisiae Gene Name(s): RPL22A YLR061W L2168
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L23-A BV, DV 137 Saccharomyces cerevisiae Gene Name(s): RPL23A Gene View RPL17A RPL17AA YBL087C YBL0713
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L24-A BW, DW 155 Saccharomyces cerevisiae Gene Name(s): RPL24A RP29 RPL30A YGL031C
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L25 BX, DX 142 Saccharomyces cerevisiae Gene Name(s): RPL25 YOL127W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L26-A BY, DY 127 Saccharomyces cerevisiae Gene Name(s): RPL26A RPL26 Gene View RPL33A YLR344W L8300.4
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L27-A BZ, DZ 136 Saccharomyces cerevisiae Gene Name(s): RPL27A Gene View RPL27 Gene View YHR010W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L28 Ba, Da 149 Saccharomyces cerevisiae Gene Name(s): RPL28 Gene View CYH2 YGL103W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L29 Bb, Db 59 Saccharomyces cerevisiae Gene Name(s): RPL29 Gene View YL43 YFR032C-A YFR032BW
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L30 Bc, Dc 105 Saccharomyces cerevisiae Gene Name(s): RPL30 Gene View RPL32 Gene View YGL030W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L31-A Bd, Dd 113 Saccharomyces cerevisiae Gene Name(s): RPL31A RPL34 Gene View RPL34A YDL075W D2478
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L32 Be, De 130 Saccharomyces cerevisiae Gene Name(s): RPL32 Gene View YBL092W YBL0838
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L33-A Bf, Df 107 Saccharomyces cerevisiae Gene Name(s): RPL33A RPL37A Gene View YPL143W LPI4W P2625
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L34-A Bg, Dg 121 Saccharomyces cerevisiae Gene Name(s): RPL34A YER056C-A YER056BC
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L35-A Bh, Dh 120 Saccharomyces cerevisiae Gene Name(s): RPL35A Gene View SOS1 Gene View YDL191W D1249
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L36-A Bi, Di 100 Saccharomyces cerevisiae Gene Name(s): RPL36A Gene View RPL39A YMR194W YM9646.06
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L37-A Bj, Dj 88 Saccharomyces cerevisiae Gene Name(s): RPL37A Gene View RPL35A Gene View YLR185W L9470.6
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L38 Bk, Dk 78 Saccharomyces cerevisiae Gene Name(s): RPL38 Gene View YLR325C L8543.2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L39 Bl, Dl 51 Saccharomyces cerevisiae Gene Name(s): RPL39 Gene View RPL46 SPB2 YJL189W J0360
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L40 Bm, Dm 128 Saccharomyces cerevisiae Gene Name(s): RPL40A UBI1 YIL148W
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L41-A Bn, Dn 25 Saccharomyces cerevisiae Gene Name(s): RPL41A RPL47A YL41A YDL184C D1290
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L42-A Bo, Do 106 Saccharomyces cerevisiae Gene Name(s): RPL42A RPL41A SCL41A YNL162W N1722
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
60S ribosomal protein L43-A Bp, Dp 92 Saccharomyces cerevisiae Gene Name(s): RPL43A YPR043W YP9499.02
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Suppressor protein STM1 Ch 273 Saccharomyces cerevisiae Mutation: A119X, E120X, K121X, E122X, A123X, Q124X, A125X, D126X, A127X, A128X, A129X, E130X, I131X, A132X, E133X, D134X, A135X, A136X, E137X, A138X, E139X, L155X, N156X, Q157X, Q158X, A159X, N160X, N161X, Q162X, F163X, N164X, K165X, V166X, P167X, E168X, A169X, K170X, K171X, V172X, E173X, L174X
Ribosomal protein L12 DK 155 Saccharomyces cerevisiae
60S acidic ribosomal protein P0 Dq 312 Saccharomyces cerevisiae Mutation: S199X, S200X, I201X, L202X, D203X, I204X, T205X, D206X, E207X, E208X, L209X, V210X, S211X, H212X, F213X, V214X, S215X, A216X, V217X, S218X, T219X, I220X, A221X
Gene Name(s): RPP0 L10E RPA0 RPL10E RPLA0 YLR340W L8300.8
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ribosomal protein P1 alpha Dr 47 Saccharomyces cerevisiae
Ribosomal protein P2 beta Ds 46 Saccharomyces cerevisiae
Macromolecule Entities
Molecule Chains Length Organism Details
18S RIBOSOMAL RNA A2 1800 Saccharomyces cerevisiae
25S rRNA A1, A5 3396 Saccharomyces cerevisiae
5S rRNA A3, A7 121 Saccharomyces cerevisiae
5.8S rRNA A4, A8 158 Saccharomyces cerevisiae
18S rRNA A6 1800 Saccharomyces cerevisiae

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
OHX
Query on OHX

A1, A2, A3, A4, A5, A6, A7, A8, AC, AI, AL, AN, AP, Ad, Ag, BA, BB, BC, BD, BI, BN, BO, BP, BR, BT, Bb, Bf, Bj, Bo, CB, CG, CI, CJ, CL, CN, CP, CS, CY, Cd, Cg, DA, DB, DC, DD, DG, DH, DI, DJ, DM, DO, DP, DQ, DR, DV, Db, De, Df, Dg, Dh, Dj, Do osmium (III) hexammine
osmium(6+) hexaazanide (Synonym)
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

Aa, Ab, Ad, Af, Bj, Bm, Bo, Bp, Ca, Cb, Cd, Cf, Dj, Dm, Do, Dp ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A1, A2, A3, A4, A5, A6, A7, A8, AB, AC, AE, AI, AJ, AL, AN, AP, AS, AX, Aa, Ad, Af, BA, BB, BC, BD, BE, BF, BG, BI, BJ, BL, BN, BO, BP, BQ, BR, BS, BT, BV, BY, Ba, Bd, Be, Bf, Bg, Bj, Bl, Bm, Bo, CB, CE, CF, CG, CI, CL, CP, CQ, CS, CX, CY, CZ, Ca, Cd, Ch, DA, DB, DC, DD, DF, DG, DH, DJ, DL, DM, DN, DO, DP, DQ, DR, DS, DT, DV, DW, DY, Da, Db, Dd, De, Df, Dg, Dj, Dl, Dm, Dn, Do, Dp, Dq MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
N
Query on N
A2, A6 RNA LINKING C5 H11 O7 P --
UNK
Query on UNK
Af, Ah, Cf, Ch, DK, Dq, Dr, Ds L-PEPTIDE LINKING C4 H9 N O2 --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.0 Å
  • R-Value Free: 0.228
  • R-Value Work: 0.181
  • Space Group: P 1 21 1

Unit Cell:

Length (Å) Angle (°)
a = 436.43 α = 90.00
b = 288.22 β = 98.99
c = 305.08 γ = 90.00

Structure Validation

View Full Validation Report



Entry History

Deposition Data

  • Deposited Date: 2011-10-11
  • Released Date: 2014-07-09
  • Deposition author(s): Ben-Shem, A., Garreau de Loubresse, N., Melnikov, S., Jenner, L., Yusupova, G., Yusupov, M.
  • Previous versions: 3U5B 3U5C 3U5D 3U5E 3U5F 3U5G 3U5H 3U5I

Revision History

  • Version 1_0: 2014-07-09

    Type: Initial release

  • Version 1_1: 2014-12-10

    Type: Other

  • Version 1_2: 2017-06-21

    Type: Database references