6GQB

Cryo-EM reconstruction of yeast 80S ribosome in complex with mRNA, tRNA and eEF2 (GDP+AlF4/sordarin)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Structural Insights into the Role of Diphthamide on Elongation Factor 2 in mRNA Reading-Frame Maintenance.

Pellegrino, S.Demeshkina, N.Mancera-Martinez, E.Melnikov, S.Simonetti, A.Myasnikov, A.Yusupov, M.Yusupova, G.Hashem, Y.

(2018) J Mol Biol 430: 2677-2687

  • DOI: 10.1016/j.jmb.2018.06.006
  • Primary Citation of Related Structures:  
    6GQ1, 6GQB, 6GQV

  • PubMed Abstract: 
  • One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species ...

    One of the most critical steps of protein biosynthesis is the coupled movement of mRNA, which encodes genetic information, with tRNAs on the ribosome. In eukaryotes, this process is catalyzed by a conserved G-protein, the elongation factor 2 (eEF2), which carries a unique post-translational modification, called diphthamide, found in all eukaryotic species. Here we present near-atomic resolution cryo-electron microscopy structures of yeast 80S ribosome complexes containing mRNA, tRNA and eEF2 trapped in different GTP-hydrolysis states which provide further structural insights into the role of diphthamide in the mechanism of translation fidelity in eukaryotes.


    Organizational Affiliation

    ARNA, U1212 Université de Bordeaux, Institut Européen de Chimie et de Biologie (IECB) Inserm, Pessac 33600, France. Electronic address: yaser.hashem@u-bordeaux.fr.



Macromolecules

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Entity ID: 4
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60S acidic ribosomal protein P0D [auth P0]189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0L10ERPA0RPL10ERPLA0YLR340WL8300.8
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Entity ID: 5
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60S ribosomal protein L12-AE [auth P2]94Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL12ARPL15BYEL054C
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Entity ID: 6
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60S ribosomal protein L2-AF [auth A]252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2ARPL5BYFR031C-AYFR031BC
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Entity ID: 7
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60S ribosomal protein L3G [auth B]386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3MAK8TCM1YOR063WYOR29-14
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Entity ID: 8
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60S ribosomal protein L4-AH [auth C]361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4ARPL2RPL2AYBR031WYBR0315
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Entity ID: 9
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60S ribosomal protein L5I [auth D]296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5RPL1RPL1AYPL131WLPI14W
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Entity ID: 10
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60S ribosomal protein L6-AJ [auth E]175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6ARPL17AYL16AYML073C
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Entity ID: 11
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60S ribosomal protein L7-AK [auth F]222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7ARPL6ARPL8AYL8AYGL076C
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Entity ID: 12
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60S ribosomal protein L8-AL [auth G]233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8AMAK7RPL4AYHL033C
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Entity ID: 13
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60S ribosomal protein L9-AM [auth H]191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9ARPL8ARPL9YGL147C
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Entity ID: 14
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60S ribosomal protein L10N [auth I]220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10GRC5QSR1YLR075W
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Entity ID: 15
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60S ribosomal protein L11-BO [auth J]169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11BRP39BRPL16BYGR085C
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Entity ID: 16
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60S ribosomal protein L13-AP [auth L]193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13AYDL082W
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Entity ID: 17
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60S ribosomal protein L14-AQ [auth M]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 18
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60S ribosomal protein L15-AR [auth N]203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15ARPL10ARPL13AYL10AYLR029C
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Entity ID: 19
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60S ribosomal protein L16-AS [auth O]197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16ARPL13RPL21AYIL133C
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60S ribosomal protein L17-AT [auth P]183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17ARPL17RPL20AYKL180W
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Entity ID: 21
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60S ribosomal protein L18-AU [auth Q]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18ARP28AYOL120C
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Entity ID: 22
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60S ribosomal protein L19-AV [auth R]188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19ARPL23AYL14AYBR084C-AYBR084BC
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Entity ID: 23
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60S ribosomal protein L20-AW [auth S]172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20ARPL18ARPL18A2YMR242CYM9408.04C
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Entity ID: 24
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60S ribosomal protein L21-AX [auth T]159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21AURP1YBR191WYBR1401
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Entity ID: 25
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60S ribosomal protein L22-AY [auth U]100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22AYLR061WL2168
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Entity ID: 26
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60S ribosomal protein L23-AZ [auth V]136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23ARPL17ARPL17AAYBL087CYBL0713
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Entity ID: 27
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60S ribosomal protein L24-AAA [auth W]64Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24ARP29RPL30AYGL031C
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Entity ID: 28
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60S ribosomal protein L25BA [auth X]121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25YOL127W
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Entity ID: 29
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60S ribosomal protein L26-ACA [auth Y]126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26ARPL26RPL33AYLR344WL8300.4
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Entity ID: 30
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60S ribosomal protein L27-ADA [auth Z]135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27ARPL27YHR010W
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Entity ID: 31
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60S ribosomal protein L28EA [auth a]148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28CYH2YGL103W
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Entity ID: 32
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60S ribosomal protein L29FA [auth b]58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29YL43YFR032C-AYFR032BW
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Entity ID: 33
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60S ribosomal protein L30GA [auth c]97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30RPL32YGL030W
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Entity ID: 34
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60S ribosomal protein L31-AHA [auth d]109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31ARPL34RPL34AYDL075WD2478
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Entity ID: 35
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60S ribosomal protein L32IA [auth e]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32YBL092WYBL0838
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Entity ID: 36
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60S ribosomal protein L33-AJA [auth f]106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33ARPL37AYPL143WLPI4WP2625
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60S ribosomal protein L34-AKA [auth g]112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34AYER056C-AYER056BC
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Entity ID: 38
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60S ribosomal protein L35-ALA [auth h]119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35ASOS1YDL191WD1249
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Entity ID: 39
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60S ribosomal protein L36-AMA [auth i]99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36ARPL39AYMR194WYM9646.06
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Entity ID: 40
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60S ribosomal protein L37-ANA [auth j]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37ARPL35AYLR185WL9470.6
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Entity ID: 41
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60S ribosomal protein L38OA [auth k]77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38YLR325CL8543.2
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Entity ID: 42
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60S ribosomal protein L39PA [auth l]50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39RPL46SPB2YJL189WJ0360
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Entity ID: 43
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Ubiquitin-60S ribosomal protein L40QA [auth m]52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40AUBI1YIL148W
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Entity ID: 44
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60S ribosomal protein L41-BRA [auth n]25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41ARPL47AYL41AYDL184CD1290
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Entity ID: 45
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60S ribosomal protein L42-ASA [auth o]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42ARPL41ASCL41AYNL162WN1722
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Entity ID: 46
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60S ribosomal protein L43-ATA [auth p]91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43AYPR043WYP9499.02
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Entity ID: 48
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40S ribosomal protein S0-AVA [auth q]206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0ANAB1NAB1AYST1YGR214W
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Entity ID: 49
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40S ribosomal protein S1-AWA [auth r]214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1APLC1RPS10AYLR441CL9753.9
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Entity ID: 50
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40S ribosomal protein S2XA [auth s]217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2RPS4SUP38SUP44YGL123WG2893
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Entity ID: 51
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40S ribosomal protein S3YA [auth t]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3SUF14YNL178WN1653
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Entity ID: 52
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40S ribosomal protein S4-AZA [auth u]260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4ARPS7BYJR145CJ2186
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Entity ID: 53
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40S ribosomal protein S5AB [auth v]206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5RPS2YJR123WJ2045
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Entity ID: 54
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40S ribosomal protein S6-ABB [auth w]223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6ARPS101RPS10BYPL090CLPG18C
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-ACB [auth x]184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7ARPS30YOR096WYOR3177W
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Entity ID: 56
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40S ribosomal protein S8-ADB [auth y]199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8ARPS14AYBL072CYBL06.05YBL0613
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Entity ID: 57
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40S ribosomal protein S9-AEB [auth z]185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS9ARPS13AYS11AYPL081W
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Entity ID: 58
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40S ribosomal protein S10-AFB [auth AA]105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10AYOR293W
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Entity ID: 59
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40S ribosomal protein S11-AGB [auth AB]153Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11ARPS18AYDR025WYD9813.03
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Entity ID: 60
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40S ribosomal protein S12HB [auth AC]124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12YOR369C
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Entity ID: 61
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40S ribosomal protein S13IB [auth AD]150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13RPS13CYDR064WD4252YD9609.18
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Entity ID: 62
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40S ribosomal protein S14-BJB [auth AE]127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14BCRY2YJL191WJ0354
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Entity ID: 63
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40S ribosomal protein S15KB [auth AF]124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS15RPS21YOL040C
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Entity ID: 64
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40S ribosomal protein S16-ALB [auth AG]141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16ARP61RYMR143WYM9375.12
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Entity ID: 65
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40S ribosomal protein S17-BMB [auth AH]125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17BRP51BYDR447C
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Entity ID: 66
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40S ribosomal protein S18-ANB [auth AI]145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18AYDR450WD9461.35
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Entity ID: 67
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40S ribosomal protein S19-AOB [auth AJ]143Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS19ARP55ARPS16AAYOL121C
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Entity ID: 68
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40S ribosomal protein S20PB [auth AK]107Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS20URP2YHL015W
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Entity ID: 69
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40S ribosomal protein S21-AQB [auth AL]87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS21ARPS25RPS25ARPS26AYKR057W
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Entity ID: 70
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40S ribosomal protein S22-ARB [auth AM]129Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS22ARPS24RPS24AYJL190CJ0355
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Entity ID: 71
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40S ribosomal protein S23-ASB [auth AN]144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23ARPS28AYGR118WG6178
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Entity ID: 72
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40S ribosomal protein S24-ATB [auth AO]134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24ARPS24EAYER074W
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Entity ID: 73
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40S ribosomal protein S25-AUB [auth AP]70Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS25ARPS31AYGR027C
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Entity ID: 74
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40S ribosomal protein S26-BVB [auth AQ]97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26BYER131W
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Entity ID: 75
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40S ribosomal protein S27-AWB [auth AR]81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27AYKL156W
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Entity ID: 76
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40S ribosomal protein S28-AXB [auth AS]63Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS28ARPS33RPS33AYOR167CO3600
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Entity ID: 77
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40S ribosomal protein S29-AYB [auth AT]53Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS29ARPS36AYS29AYLR388WL8084.11
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Entity ID: 78
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40S ribosomal protein S30-AZB [auth AU]60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30AYLR287C-AL8003.23YLR287BC
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Entity ID: 79
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Guanine nucleotide-binding protein subunit beta-like proteinAC [auth AV]318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: ASC1CPC2YMR116CYM9718.15C
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Entity ID: 80
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Ubiquitin-40S ribosomal protein S31BC [auth AW]37Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS31RPS37UBI3YLR167WL9470.14
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Entity ID: 83
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60S ribosomal protein L1-AEC [auth BA]204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1ASSM1SSM1AYPL220W
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Entity ID: 84
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 2FC [auth AZ]840Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EFT1YOR133WO3317YOR3317WEFT2YDR385W
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNAA [auth 1]3396Saccharomyces cerevisiae S288C
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Entity ID: 2
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5S ribosomal RNAB [auth 3]121Saccharomyces cerevisiae S288C
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Entity ID: 3
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5.8S ribosomal RNAC [auth 4]158Saccharomyces cerevisiae S288C
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Entity ID: 47
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18S ribosomal RNAUA [auth 2]1797Saccharomyces cerevisiae S288C
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Entity ID: 81
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Transfer RNA - PheCC [auth AX]76Saccharomyces cerevisiae S288C
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  • Entity ID: 82
    MoleculeChainsLengthOrganismImage
    Messenger RNADC [auth AY]7Saccharomyces cerevisiae S288C
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    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO1 (Subject of Investigation/LOI)
    Query on SO1

    Download Ideal Coordinates CCD File 
    OC [auth AZ][1R-(1.ALPHA.,3A.BETA.,4.BETA.,4A.BETA.,7.BETA.,7A.ALPHA.,8A.BETA.)]8A-[(6-DEOXY-4-O-METHYL-BETA-D-ALTROPYRANOSYLOXY)METHYL]-4-FORMYL-4,4A,5,6,7,7A,8,8A-OCTAHYDRO-7-METHYL-3-(1-METHYLETHYL)-1,4-METHANO-S-INDACENE-3A(1H)-CARBOXYLIC ACID
    C27 H42 O8
    DIBGPTPYRVEPSP-OHFCZZTFSA-N
     Ligand Interaction
    GDP (Subject of Investigation/LOI)
    Query on GDP

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    PC [auth AZ]GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N
     Ligand Interaction
    ALF
    Query on ALF

    Download Ideal Coordinates CCD File 
    QC [auth AZ]TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J
     Ligand Interaction
    ZN
    Query on ZN

    Download Ideal Coordinates CCD File 
    GC [auth j], HC [auth m], IC [auth o], JC [auth p], KC [auth AQ], LC [auth AR], MC [auth AT], NC [auth AW]ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N
     Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    DDE
    Query on DDE
    FC [auth AZ]L-PEPTIDE LINKINGC13 H24 N5 O3HIS
    Experimental Data & Validation

    Experimental Data

    • Method: ELECTRON MICROSCOPY
    • Resolution: 3.90 Å
    • Aggregation State: PARTICLE 
    • Reconstruction Method: SINGLE PARTICLE 

    Structure Validation

    View Full Validation Report




    Entry History & Funding Information

    Deposition Data


    Funding OrganizationLocationGrant Number
    FranceANR-15-CE11-0021-01
    FranceFRM-DBF20160635745
    ERC-294312
    FranceANR-14-ACHN-0024

    Revision History  (Full details and data files)

    • Version 1.0: 2018-07-11
      Type: Initial release
    • Version 1.1: 2018-07-18
      Changes: Data collection, Database references
    • Version 1.2: 2018-08-08
      Changes: Data collection, Database references
    • Version 1.3: 2018-11-28
      Changes: Data collection, Database references
    • Version 1.4: 2021-08-04
      Changes: Derived calculations, Other