4V88

The structure of the eukaryotic ribosome at 3.0 A resolution.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.229 
  • R-Value Work: 0.181 
  • R-Value Observed: 0.182 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

The structure of the eukaryotic ribosome at 3.0 angstrom resolution.

Ben-Shem, A.Garreau de Loubresse, N.Melnikov, S.Jenner, L.Yusupova, G.Yusupov, M.

(2011) Science 334: 1524-1529

  • DOI: 10.1126/science.1212642
  • Primary Citation of Related Structures:  
    4V88

  • PubMed Abstract: 
  • Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts. We report the crystal structure of the 80S ribosome from the yeast Saccharomyces cerevisiae--including nearly all ribosomal RNA bases and protein side chains as well as an additional protein, Stm1--at a resolution of 3 ...

    Ribosomes translate genetic information encoded by messenger RNA into proteins. Many aspects of translation and its regulation are specific to eukaryotes, whose ribosomes are much larger and intricate than their bacterial counterparts. We report the crystal structure of the 80S ribosome from the yeast Saccharomyces cerevisiae--including nearly all ribosomal RNA bases and protein side chains as well as an additional protein, Stm1--at a resolution of 3.0 angstroms. This atomic model reveals the architecture of eukaryote-specific elements and their interaction with the universally conserved core, and describes all eukaryote-specific bridges between the two ribosomal subunits. It forms the structural framework for the design and analysis of experiments that explore the eukaryotic translation apparatus and the evolutionary forces that shaped it.


    Organizational Affiliation

    Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch F-67400, France. adam@igbmc.fr



Macromolecules

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S0-AB [auth AA], CC [auth CA]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 3
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40S ribosomal protein S1-AC [auth AB], DC [auth CB]255Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S2D [auth AC], EC [auth CC]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S3E [auth AD], FC [auth CD]240Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S4-AF [auth AE], GC [auth CE]261Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 7
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40S ribosomal protein S5G [auth AF], HC [auth CF]225Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 8
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40S ribosomal protein S6-AH [auth AG], IC [auth CG]236Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 9
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40S ribosomal protein S7-AI [auth AH], JC [auth CH]190Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 10
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40S ribosomal protein S8-AJ [auth AI], KC [auth CI]200Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 11
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40S ribosomal protein S9-AK [auth AJ], LC [auth CJ]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 12
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40S ribosomal protein S10-AL [auth AK], MC [auth CK]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 13
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40S ribosomal protein S11-AM [auth AL], NC [auth CL]156Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 14
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40S ribosomal protein S12N [auth AM], OC [auth CM]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 15
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40S ribosomal protein S13O [auth AN], PC [auth CN]151Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 16
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40S ribosomal protein S14-AP [auth AO], QC [auth CO]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14ACRY1RPL59YCR031CYCR31C
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Entity ID: 17
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40S ribosomal protein S15Q [auth AP], RC [auth CP]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 18
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40S ribosomal protein S16-AR [auth AQ], SC [auth CQ]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 19
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40S ribosomal protein S17-AS [auth AR], TC [auth CR]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17ARP51AYML024W
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Entity ID: 20
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40S ribosomal protein S18-AT [auth AS], UC [auth CS]146Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 21
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40S ribosomal protein S19-AU [auth AT], VC [auth CT]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 22
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40S ribosomal protein S20V [auth AU], WC [auth CU]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 23
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40S ribosomal protein S21-AW [auth AV], XC [auth CV]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 24
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40S ribosomal protein S22-AX [auth AW], YC [auth CW]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 25
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40S ribosomal protein S23-AY [auth AX], ZC [auth CX]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 26
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40S ribosomal protein S24-AZ [auth AY], AD [auth CY]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 27
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40S ribosomal protein S25-AAA [auth AZ], BD [auth CZ]108Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S26-ABA [auth Aa], CD [auth Ca]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26ARPS26YGL189CG1355
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Entity ID: 29
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40S ribosomal protein S27-ACA [auth Ab], DD [auth Cb]82Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S28-ADA [auth Ac], ED [auth Cc]67Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 31
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40S ribosomal protein S29-AEA [auth Ad], FD [auth Cd]56Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 32
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40S ribosomal protein S30-AFA [auth Ae], GD [auth Ce]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 33
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40S ribosomal protein S31GA [auth Af], HD [auth Cf]152Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 34
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Guanine nucleotide-binding protein subunit beta-like protein (ASC1, RACK1)HA [auth Ag], ID [auth Cg]319Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
Suppressor protein STM1IA [auth Ah]273Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: STM1MPT4STO1YLR150WL9634.1
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Entity ID: 39
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60S ribosomal protein L2-AMA [auth BA], ND [auth DA]254Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 40
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60S ribosomal protein L3NA [auth BB], OD [auth DB]387Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 41
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60S ribosomal protein L4-AOA [auth BC], PD [auth DC]362Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 42
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60S ribosomal protein L5PA [auth BD], QD [auth DD]297Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 43
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60S ribosomal protein L6-AQA [auth BE], RD [auth DE]176Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 44
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60S ribosomal protein L7-ARA [auth BF], SD [auth DF]244Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 45
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60S ribosomal protein L8-ASA [auth BG], TD [auth DG]256Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 46
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60S ribosomal protein L9-ATA [auth BH], UD [auth DH]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 47
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60S ribosomal protein L10UA [auth BI], VD [auth DI]221Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 48
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60S ribosomal protein L11-AVA [auth BJ], WD [auth DJ]174Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11ARP39ARPL16AYPR102CP8283.14
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Entity ID: 49
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60S ribosomal protein L13-AWA [auth BL], YD [auth DL]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 50
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60S ribosomal protein L14-AXA [auth BM], ZD [auth DM]138Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 51
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60S ribosomal protein L15-AYA [auth BN], AE [auth DN]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 52
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60S ribosomal protein L16-A, 60S ribosomal protein L16-BZA [auth BO], BE [auth DO]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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Entity ID: 53
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60S ribosomal protein L17-AAB [auth BP], CE [auth DP]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 54
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L18-ABB [auth BQ], DE [auth DQ]186Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 55
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60S ribosomal protein L19-ACB [auth BR], EE [auth DR]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 56
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60S ribosomal protein L20-ADB [auth BS], FE [auth DS]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 57
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L21-AEB [auth BT], GE [auth DT]160Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 58
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60S ribosomal protein L22-AFB [auth BU], HE [auth DU]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 59
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60S ribosomal protein L23-AGB [auth BV], IE [auth DV]137Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L24-AHB [auth BW], JE [auth DW]155Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 61
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60S ribosomal protein L25IB [auth BX], KE [auth DX]142Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 62
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60S ribosomal protein L26-AJB [auth BY], LE [auth DY]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 63
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60S ribosomal protein L27-AKB [auth BZ], ME [auth DZ]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 64
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60S ribosomal protein L28LB [auth Ba], NE [auth Da]149Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 65
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60S ribosomal protein L29MB [auth Bb], OE [auth Db]59Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 66
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60S ribosomal protein L30NB [auth Bc], PE [auth Dc]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 67
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60S ribosomal protein L31-AOB [auth Bd], QE [auth Dd]113Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 68
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60S ribosomal protein L32PB [auth Be], RE [auth De]130Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 69
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60S ribosomal protein L33-AQB [auth Bf], SE [auth Df]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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Entity ID: 70
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60S ribosomal protein L34-ARB [auth Bg], TE [auth Dg]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 71
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60S ribosomal protein L35-ASB [auth Bh], UE [auth Dh]120Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-ATB [auth Bi], VE [auth Di]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 73
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60S ribosomal protein L37-AUB [auth Bj], WE [auth Dj]88Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 74
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60S ribosomal protein L38VB [auth Bk], XE [auth Dk]78Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39WB [auth Bl], YE [auth Dl]51Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L40XB [auth Bm], ZE [auth Dm]128Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 77
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60S ribosomal protein L41-AYB [auth Bn], AF [auth Dn]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 78
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60S ribosomal protein L42-AZB [auth Bo], BF [auth Do]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-AAC [auth Bp], CF [auth Dp]92Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 81
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Suppressor protein STM1JD [auth Ch]273Saccharomyces cerevisiae S288CMutation(s): 0 
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Entity ID: 82
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Ribosomal protein L12XD [auth DK]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 83
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60S acidic ribosomal protein P0DF [auth Dq]312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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Entity ID: 84
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Ribosomal protein P1 alphaEF [auth Dr]47Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 85
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Ribosomal protein P2 betaFF [auth Ds]46Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
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18S RIBOSOMAL RNAA [auth A2]1800Saccharomyces cerevisiae
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Entity ID: 36
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25S rRNAJA [auth A1], KD [auth A5]3396Saccharomyces cerevisiae
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Entity ID: 37
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5S rRNAKA [auth A3], LD [auth A7]121Saccharomyces cerevisiae
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Entity ID: 38
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5.8S rRNALA [auth A4], MD [auth A8]158Saccharomyces cerevisiae
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Entity ID: 80
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18S rRNABC [auth A6]1800Saccharomyces cerevisiae
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Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OHX
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