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 1.3 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, 6GQV, 6GQB

  • 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
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0 P0189Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPP0, L10E, RPA0, RPL10E, RPLA0, YLR340W, L8300.8
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Entity ID: 5
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60S ribosomal protein L12-A P294Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL12A, RPL15B, YEL054C
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 6
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60S ribosomal protein L2-A A252Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL2A, RPL5B, YFR031C-A, YFR031BC
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Entity ID: 7
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60S ribosomal protein L3 B386Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL3, MAK8, TCM1, YOR063W, YOR29-14
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Entity ID: 8
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60S ribosomal protein L4-A C361Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL4A, RPL2, RPL2A, YBR031W, YBR0315
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Entity ID: 9
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60S ribosomal protein L5 D296Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL5, RPL1, RPL1A, YPL131W, LPI14W
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Entity ID: 10
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60S ribosomal protein L6-A E175Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL6A, RPL17A, YL16A, YML073C
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Entity ID: 11
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60S ribosomal protein L7-A F222Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL7A, RPL6A, RPL8A, YL8A, YGL076C
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Entity ID: 12
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60S ribosomal protein L8-A G233Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL8A, MAK7, RPL4A, YHL033C
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Entity ID: 13
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60S ribosomal protein L9-A H191Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL9A, RPL8A, RPL9, YGL147C
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Entity ID: 14
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60S ribosomal protein L10 I220Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL10, GRC5, QSR1, YLR075W
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Entity ID: 15
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60S ribosomal protein L11-B J169Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL11B, RP39B, RPL16B, YGR085C
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Entity ID: 16
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60S ribosomal protein L13-A L193Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL13A, YDL082W
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Entity ID: 17
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60S ribosomal protein L14-A M136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL14A, YKL006W, YKL153
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Entity ID: 18
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60S ribosomal protein L15-A N203Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL15A, RPL10A, RPL13A, YL10A, YLR029C
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Entity ID: 19
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60S ribosomal protein L16-A O197Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL16A, RPL13, RPL21A, YIL133C
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Entity ID: 20
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60S ribosomal protein L17-A P183Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL17A, RPL17, RPL20A, YKL180W
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Entity ID: 21
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60S ribosomal protein L18-A Q185Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL18A, RP28A, YOL120C
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Entity ID: 22
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60S ribosomal protein L19-A R188Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL19A, RPL23A, YL14A, YBR084C-A, YBR084BC
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Entity ID: 23
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60S ribosomal protein L20-A S172Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL20A, RPL18A, RPL18A2, YMR242C, YM9408.04C
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Entity ID: 24
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60S ribosomal protein L21-A T159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL21A, URP1, YBR191W, YBR1401
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Entity ID: 25
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60S ribosomal protein L22-A U100Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL22A, YLR061W, L2168
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Entity ID: 26
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60S ribosomal protein L23-A V136Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL23A, RPL17A, RPL17AA, YBL087C, YBL0713
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Entity ID: 27
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60S ribosomal protein L24-A W64Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL24A, RP29, RPL30A, YGL031C
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Entity ID: 28
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60S ribosomal protein L25 X121Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL25, YOL127W
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Entity ID: 29
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60S ribosomal protein L26-A Y126Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL26A, RPL26, RPL33A, YLR344W, L8300.4
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Entity ID: 30
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60S ribosomal protein L27-A Z135Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL27A, RPL27, YHR010W
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 31
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60S ribosomal protein L28 a148Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL28, CYH2, YGL103W
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Entity ID: 32
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60S ribosomal protein L29 b58Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL29, YL43, YFR032C-A, YFR032BW
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Entity ID: 33
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60S ribosomal protein L30 c97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL30, RPL32, YGL030W
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Entity ID: 34
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60S ribosomal protein L31-A d109Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL31A, RPL34, RPL34A, YDL075W, D2478
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Entity ID: 35
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60S ribosomal protein L32 e127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL32, YBL092W, YBL0838
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Entity ID: 36
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60S ribosomal protein L33-A f106Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL33A, RPL37A, YPL143W, LPI4W, P2625
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Entity ID: 37
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60S ribosomal protein L34-A g112Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL34A, YER056C-A, YER056BC
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Entity ID: 38
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60S ribosomal protein L35-A h119Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL35A, SOS1, YDL191W, D1249
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Entity ID: 39
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60S ribosomal protein L36-A i99Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL36A, RPL39A, YMR194W, YM9646.06
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Entity ID: 40
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60S ribosomal protein L37-A j87Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL37A, RPL35A, YLR185W, L9470.6
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Entity ID: 41
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60S ribosomal protein L38 k77Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL38, YLR325C, L8543.2
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Entity ID: 42
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60S ribosomal protein L39 l50Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL39, RPL46, SPB2, YJL189W, J0360
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Entity ID: 43
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Ubiquitin-60S ribosomal protein L40 m52Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
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Entity ID: 44
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60S ribosomal protein L41-B n25Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL41A, RPL47A, YL41A, YDL184C, D1290
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Entity ID: 45
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60S ribosomal protein L42-A o105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL42A, RPL41A, SCL41A, YNL162W, N1722
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Entity ID: 46
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60S ribosomal protein L43-A p91Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL43A, YPR043W, YP9499.02
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Entity ID: 48
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40S ribosomal protein S0-A q206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS0A, NAB1, NAB1A, YST1, YGR214W
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Entity ID: 49
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40S ribosomal protein S1-A r214Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS1A, PLC1, RPS10A, YLR441C, L9753.9
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Entity ID: 50
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40S ribosomal protein S2 s217Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS2, RPS4, SUP38, SUP44, YGL123W, G2893
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Entity ID: 51
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40S ribosomal protein S3 t223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS3, SUF14, YNL178W, N1653
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Entity ID: 52
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40S ribosomal protein S4-A u260Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS4A, RPS7B, YJR145C, J2186
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Entity ID: 53
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40S ribosomal protein S5 v206Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS5, RPS2, YJR123W, J2045
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Entity ID: 54
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40S ribosomal protein S6-A w223Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS6A, RPS101, RPS10B, YPL090C, LPG18C
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Entity ID: 55
MoleculeChainsSequence LengthOrganismDetailsImage
40S ribosomal protein S7-A x184Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS7A, RPS30, YOR096W, YOR3177W
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Entity ID: 56
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40S ribosomal protein S8-A y199Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS8A, RPS14A, YBL072C, YBL06.05, YBL0613
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Entity ID: 57
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40S ribosomal protein S9-A z185Saccharomyces 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: 58
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40S ribosomal protein S10-A AA105Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS10A, YOR293W
Find proteins for Q08745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 59
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40S ribosomal protein S11-A AB153Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS11A, RPS18A, YDR025W, YD9813.03
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Entity ID: 60
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40S ribosomal protein S12 AC124Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS12, YOR369C
Find proteins for P48589 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 61
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40S ribosomal protein S13 AD150Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS13, RPS13C, YDR064W, D4252, YD9609.18
Find proteins for P05756 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 62
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40S ribosomal protein S14-B AE127Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS14B, CRY2, YJL191W, J0354
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Entity ID: 63
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40S ribosomal protein S15 AF124Saccharomyces 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: 64
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40S ribosomal protein S16-A AG141Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS16A, RP61R, YMR143W, YM9375.12
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Entity ID: 65
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40S ribosomal protein S17-B AH125Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS17B, RP51B, YDR447C
Find proteins for P14127 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 66
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40S ribosomal protein S18-A AI145Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS18A, YDR450W, D9461.35
Find proteins for P0CX55 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 67
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40S ribosomal protein S19-A AJ143Saccharomyces 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: 68
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40S ribosomal protein S20 AK107Saccharomyces 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: 69
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40S ribosomal protein S21-A AL87Saccharomyces 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: 70
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40S ribosomal protein S22-A AM129Saccharomyces 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: 71
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40S ribosomal protein S23-A AN144Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS23A, RPS28A, YGR118W, G6178
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Entity ID: 72
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40S ribosomal protein S24-A AO134Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS24A, RPS24EA, YER074W
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Entity ID: 73
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40S ribosomal protein S25-A AP70Saccharomyces 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: 74
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40S ribosomal protein S26-B AQ97Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS26B, YER131W
Find proteins for P39939 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 75
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40S ribosomal protein S27-A AR81Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS27A, YKL156W
Find proteins for P35997 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
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40S ribosomal protein S28-A AS63Saccharomyces 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: 77
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40S ribosomal protein S29-A AT53Saccharomyces 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: 78
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40S ribosomal protein S30-A AU60Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPS30A, YLR287C-A, L8003.23, YLR287BC
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Entity ID: 79
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Guanine nucleotide-binding protein subunit beta-like protein AV318Saccharomyces 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: 80
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Ubiquitin-40S ribosomal protein S31 AW37Saccharomyces 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: 83
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60S ribosomal protein L1-A BA204Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: RPL1A, SSM1, SSM1A, YPL220W
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Entity ID: 84
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Elongation factor 2 AZ840Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: EFT1, YOR133W, O3317, YOR3317W, EFT2, YDR385W
Find proteins for P32324 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
MoleculeChainsLengthOrganismImage
Saccharomyces cerevisiae S288C 35S pre-ribosomal RNA (RDN37-1), miscRNA13396Saccharomyces cerevisiae S288C
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Entity ID: 2
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5S ribosomal RNA3121Saccharomyces cerevisiae S288C
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Entity ID: 3
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5.8S ribosomal RNA4158Saccharomyces cerevisiae S288C
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Entity ID: 47
MoleculeChainsLengthOrganismImage
18S ribosomal RNA21797Saccharomyces cerevisiae S288C
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Entity ID: 81
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Transfer RNA - PheAX76Saccharomyces cerevisiae S288C
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    • Entity ID: 82
    MoleculeChainsLengthOrganismImage
    Messenger RNAAY7Saccharomyces cerevisiae S288C
    Small Molecules
    Ligands 4 Unique
    IDChainsName / Formula / InChI Key2D Diagram3D Interactions
    SO1
    Query on SO1
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    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
    Query on GDP
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    AZ
    		GUANOSINE-5'-DIPHOSPHATE
    C10 H15 N5 O11 P2
    QGWNDRXFNXRZMB-UUOKFMHZSA-N    		 Ligand Interaction
    ALF
    Query on ALF
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    AZ
    		TETRAFLUOROALUMINATE ION
    Al F4
    UYOMQIYKOOHAMK-UHFFFAOYSA-J    		 Ligand Interaction
    ZN
    Query on ZN
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    AQ, AR, AT, AW, j, m, o, p
    		ZINC ION
    Zn
    PTFCDOFLOPIGGS-UHFFFAOYSA-N    		 Ligand Interaction
    Modified Residues  1 Unique
    IDChainsTypeFormula2D DiagramParent
    DDE
    Query on DDE    		AZL-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

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    View more in-depth experimental data

    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