4U4R

Crystal structure of Lactimidomycin bound to the yeast 80S ribosome

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history. 


Literature

Structural basis for the inhibition of the eukaryotic ribosome.

Garreau de Loubresse, N., Prokhorova, I., Holtkamp, W., Rodnina, M.V., Yusupova, G., Yusupov, M.

(2014) Nature 513: 517-522

  • DOI: 10.1038/nature13737
  • Structures With Same Primary Citation

  • PubMed Abstract: 

    • The ribosome is a molecular machine responsible for protein synthesis and a major target for small-molecule inhibitors. Compared to the wealth of structural information available on ribosome-targeting antibiotics in bacteria, our understanding of the ...

    The ribosome is a molecular machine responsible for protein synthesis and a major target for small-molecule inhibitors. Compared to the wealth of structural information available on ribosome-targeting antibiotics in bacteria, our understanding of the binding mode of ribosome inhibitors in eukaryotes is currently limited. Here we used X-ray crystallography to determine 16 high-resolution structures of 80S ribosomes from Saccharomyces cerevisiae in complexes with 12 eukaryote-specific and 4 broad-spectrum inhibitors. All inhibitors were found associated with messenger RNA and transfer RNA binding sites. In combination with kinetic experiments, the structures suggest a model for the action of cycloheximide and lactimidomycin, which explains why lactimidomycin, the larger compound, specifically targets the first elongation cycle. The study defines common principles of targeting and resistance, provides insights into translation inhibitor mode of action and reveals the structural determinants responsible for species selectivity which could guide future drug development.

    Organizational Affiliation: 

    Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U964, CNRS UMR7104, Université de Strasbourg, 67404, Illkirch, France.



Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S1-AS1, s1254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
Find proteins for P33442 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S2S2, s2253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
Find proteins for P25443 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S4-AS4, s4260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
Find proteins for P0CX35 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S5S5, s5224Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
Find proteins for P26783 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S8-AS8, s8200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
Find proteins for P0CX39 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S9-AS9, s9196Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9A, RPS13A, YS11A, YPL081W
Find proteins for O13516 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S11-AC1, c1155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S12C2, c2142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S13C3, c3150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S14-AC4, c4136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14A, CRY1, RPL59, YCR031C, YCR31C
Find proteins for P06367 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S15C5, c5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15, RPS21, YOL040C
Find proteins for Q01855 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S16-AC6, c6142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
Find proteins for P0CX51 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S18-AC8, c8145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S19-AC9, c9143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19A, RP55A, RPS16AA, YOL121C
Find proteins for P07280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S21-AD1, d187Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21A, RPS25, RPS25A, RPS26A, YKR057W
Find proteins for P0C0V8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S24-AD4, d4134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
Find proteins for P0CX31 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S25-AD5, d5107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25A, RPS31A, YGR027C
Find proteins for Q3E792 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S26-BD6, d697Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26B, YER131W
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S27-AD7, d781Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S28-AD8, d866Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28A, RPS33, RPS33A, YOR167C, O3600
Find proteins for Q3E7X9 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S29-AD9, d955Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29A, RPS36A, YS29A, YLR388W, L8084.11
Find proteins for P41057 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-AE060Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
Guanine nucleotide-binding protein subunit beta-like proteinSR, sR318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1, CPC2, YMR116C, YM9718.15C
Find proteins for P38011 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
Suppressor protein STM1SM, sM273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1, MPT4, STO1, YLR150W, L9634.1
Find proteins for P39015 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AL2, l2253Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3L3, l3386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AL4, l4361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5L5, l5296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AL6, l6175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AL7, l7243Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-AL9, l9191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10M0, m0220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10, GRC5, QSR1, YLR075W
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-BM1, m1173Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11B, RP39B, RPL16B, YGR085C
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AM3, m3198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AM4, m4137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-AM5, m5203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AM6, m6198Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
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Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-AM7, m7183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AM8, m8185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-AM9, m9188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
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Entity ID: 56
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AN0, n0172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-AN1, n1159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
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Entity ID: 58
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-AN2, n2120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 59
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-AN3, n3136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-AN4, n4155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24A, RP29, RPL30A, YGL031C
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25N5, n5141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
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Entity ID: 62
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-AN6, n6126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-AN7, n7135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28N8, n8148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29N9, n958Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29, YL43, YFR032C-A, YFR032BW
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30O0, o0104Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-AO1, o1112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32O2, o2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-AO3, o3106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-AO4, o4119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-AO5, o5119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-AO6, o699Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-AO7, o787Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38O8, o877Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39O9, o950Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40Q0, q052Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L41-AQ1, q125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41A, RPL47A, YL41A, YDL184C, D1290
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Entity ID: 80
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S30-Ae062Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
Find proteins for P0CX33 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 82
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0p0311Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 83
MoleculeChainsSequence LengthOrganismDetails
Unknown protein p1p147Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S10-AC0, c0105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10A, YOR293W
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S17-AC7, c7136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17A, RP51A, YML024W
Find proteins for P02407 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S0-AS0, s0251Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
Find proteins for P32905 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S20D0, d0120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20, URP2, YHL015W
Find proteins for P38701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S22-AD2, d2129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22A, RPS24, RPS24A, YJL190C, J0355
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S23-AD3, d3144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
Find proteins for P0CX29 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-40S ribosomal protein S31E1, e176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31, RPS37, UBI3, YLR167W, L9470.14
Find proteins for P05759 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AL8, l8255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S3S3, s3239Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
Find proteins for P05750 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AQ2, q2105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42A, RPL41A, SCL41A, YNL162W, N1722
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AQ3, q391Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S6-AS6, s6236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
Find proteins for P0CX37 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 81
MoleculeChainsSequence LengthOrganismDetails
Unknown protein m2m2160Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetails
Unknown protein p2p246Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
40S ribosomal protein S7-AS7, s7189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
Find proteins for P26786 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganism
18S ribosomal RNA2, 61800Saccharomyces cerevisiae S288C

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Entity ID: 36
MoleculeChainsLengthOrganism
25S ribosomal RNA1, 53396Saccharomyces cerevisiae S288C

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Entity ID: 37
MoleculeChainsLengthOrganism
5S ribosomal RNA3, 7121Saccharomyces cerevisiae S288C

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Entity ID: 38
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4, 8158Saccharomyces cerevisiae S288C
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
3H3
Query on 3H3
Download CCD File 
1, 5
4-{(2R,5S,6E)-2-hydroxy-5-methyl-7-[(2R,3S,4E,6Z,10E)-3-methyl-12-oxooxacyclododeca-4,6,10-trien-2-yl]-4-oxooct-6-en-1-yl}piperidine-2,6-dione
C26 H35 N O6
OYOKHBHOTQDIPM-UGGBQLGDSA-N		 Ligand Interaction
OHX
Query on OHX
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, C1, C3, C5, C8, D9, L3, L4, L6, M0, M5, M6, M7, M9, N9, O2, O3, O7, O9, Q2, S8, SR, c1, c3, c5, c8, d4, d9, l3, l4, l5, l9, m0, m1, m4, m5, m6, m7, m8, n3, n9, o2, o3, o4, o7, q2, s1, s4, s8, s9, sR
osmium (III) hexammine
H12 N6 Os
OWCQTVJQFLTQTE-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
Download CCD File 
D6, D7, D9, E1, O7, Q0, Q2, Q3, d6, d7, d9, e1, o7, q0, q2, q3
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download CCD File 
1, 2, 3, 4, 5, 6, 7, 8, C3, L2, L3, L4, L5, L6, L7, L8, M0, M1, M3, M5, M6, M7, M9, N0, N3, N5, N8, O3, O4, O7, Q2, S8, SM, c1, c7, c8, d2, d3, d6, l2, l3, l4, l5, l7, m1, m4, m5, m6, m7, n0, n3, n6, n8, n9, o1, o3, o4, q0, q1, q3, s1, s6, s8, sM
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 436.64α = 90
b = 287.69β = 98.98
c = 304.39γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
PHENIXrefinement
PDB_EXTRACTdata extraction
XSCALEdata scaling
XSCALEdata reduction

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-22
    Type: Initial release
  • Version 1.1: 2014-12-10
    Changes: Other
  • Version 1.2: 2014-12-17
    Changes: Other
  • Version 1.3: 2015-01-14
    Changes: Database references
  • Version 1.4: 2016-01-27
    Changes: Structure summary
  • Version 1.5: 2018-07-18
    Changes: Advisory, Data collection, Derived calculations, Source and taxonomy