6I7O

The structure of a di-ribosome (disome) as a unit for RQC and NGD quality control pathways recognition.


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways.

Ikeuchi, K.Tesina, P.Matsuo, Y.Sugiyama, T.Cheng, J.Saeki, Y.Tanaka, K.Becker, T.Beckmann, R.Inada, T.

(2019) EMBO J 38

  • DOI: 10.15252/embj.2018100276
  • Primary Citation of Related Structures:  
    6I7O

  • PubMed Abstract: 
  • Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome ...

    Ribosome stalling triggers quality control pathways targeting the mRNA (NGD: no-go decay) and the nascent polypeptide (RQC: ribosome-associated quality control). RQC requires Hel2-dependent uS10 ubiquitination and the RQT complex in yeast. Here, we report that Hel2-dependent uS10 ubiquitination and Slh1/Rqt2 are crucial for RQC and NGD induction within a di-ribosome (disome) unit, which consists of the leading stalled ribosome and the following colliding ribosome. Hel2 preferentially ubiquitinated a disome over a monosome on a quality control inducing reporter mRNA in an in vitro translation reaction. Cryo-EM analysis of the disome unit revealed a distinct structural arrangement suitable for recognition and modification by Hel2. The absence of the RQT complex or uS10 ubiquitination resulted in the elimination of NGD within the disome unit. Instead, we observed Hel2-mediated cleavages upstream of the disome, governed by initial Not4-mediated monoubiquitination of eS7 and followed by Hel2-mediated K63-linked polyubiquitination. We propose that Hel2-mediated ribosome ubiquitination is required both for canonical NGD (NGD RQC + ) and RQC coupled to the disome and that RQC-uncoupled NGD outside the disome (NGD RQC - ) can occur in a Not4-dependent manner.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan beckmann@genzentrum.lmu.de tinada@m.tohoku.ac.jp.



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60S ribosomal protein L2-AD [auth AW], MD [auth XW]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3E [auth BA], ND [auth YA]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-AF [auth BE], OD [auth YE]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5G [auth BI], PD [auth YI]294Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AH [auth BM], QD [auth YM]176Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AI [auth BO], RD [auth YO]223Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AJ [auth AA], SD [auth XA]231Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AK [auth AD], TD [auth XD]190Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10L [auth BD], UD [auth YD]221Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BM [auth AG], VD [auth XG]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AN [auth AJ], WD [auth XJ]194Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AO [auth AM], XD [auth XM]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AP [auth AQ], YD [auth XQ]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AQ [auth AU], ZD [auth XU]197Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-AS [auth P], CC [auth Pb]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AT [auth Q], DC [auth Qb]216Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2U [auth R], EC [auth Rb]217Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3V [auth A], FC [auth Ab]223Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AW [auth S], GC [auth Sb]260Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S5X [auth B], HC [auth Bb]206Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AY [auth T], IC [auth Tb]218Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AZ [auth U], JC [auth Ub]185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-AAA [auth V], KC [auth Vb]200Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-ABA [auth W], LC [auth Wb]185Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-ACA [auth C], MC [auth Cb]92Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-ADA [auth X], NC [auth Xb]146Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12EA [auth D], OC [auth Db]124Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13FA [auth Y], PC [auth Yb]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-BGA [auth Z], QC [auth Zb]128Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15HA [auth E], RC [auth Eb]119Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AIA [auth F], SC [auth Fb]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S17-AJA [auth G], TC [auth Gb]125Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S18-AKA [auth H], UC [auth Hb]145Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S19-ALA [auth I], VC [auth Ib]143Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S20MA [auth J], WC [auth Jb]101Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S21-ANA [auth a], XC [auth ab]87Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S22-AOA [auth b], YC [auth bb]129Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S23-APA [auth c], ZC [auth cb]144Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S24-AQA [auth d], AD [auth db]134Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S25-ARA [auth K], BD [auth Kb]69Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S26-BSA [auth e], CD [auth eb]97Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S27-ATA [auth f], DD [auth fb]81Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S28-AUA [auth L], ED [auth Lb]63Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S29-AVA [auth M], FD [auth Mb]53Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S30-AWA [auth g], GD [auth gb]60Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-40S ribosomal protein S31XA [auth N], HD [auth Nb]73Saccharomyces cerevisiaeMutation(s): 0 
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Guanine nucleotide-binding protein subunit beta-like proteinYA [auth O], ID [auth Ob]313Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AZA [auth AX], AE [auth XX]184Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AAB [auth BB], BE [auth YB]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-ABB [auth BF], CE [auth YF]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-ACB [auth BH], DE [auth YH]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-ADB [auth BJ], EE [auth YJ]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AEB [auth BL], FE [auth YL]98Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AFB [auth AB], GE [auth XB]134Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AGB [auth AE], HE [auth XE]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 60
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L25HB [auth AH], IE [auth XH]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 61
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60S ribosomal protein L26-AIB [auth AK], JE [auth XK]124Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 62
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60S ribosomal protein L27-AJB [auth AN], KE [auth XN]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L28KB [auth AR], LE [auth XR]148Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 64
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L29LB [auth AV], ME [auth XV]58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L30MB [auth AY], NE [auth XY]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L31-ANB [auth BC], OE [auth YC]109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L32OB [auth BG], PE [auth YG]127Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 68
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L33-APB [auth BK], QE [auth YK]106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 69
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-AQB [auth BN], RE [auth YN]112Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 70
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L35-ARB [auth BP], SE [auth YP]119Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 71
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L36-ASB [auth AC], TE [auth XC]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L37-ATB [auth AF], UE [auth XF]82Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 73
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L38UB [auth AI], VE [auth XI]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L39VB [auth AL], WE [auth XL]50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
MoleculeChainsSequence LengthOrganismDetailsImage
Ubiquitin-60S ribosomal protein L40WB [auth AO], XE [auth XO]52Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 76
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L41-BXB [auth AS], YE [auth XS]25Saccharomyces cerevisiaeMutation(s): 0 
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Find proteins for P0CX87 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 77
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L42-AYB [auth AP], ZE [auth XP]105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L43-AZB [auth AT], AF [auth XT]91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
MoleculeChainsSequence LengthOrganismDetailsImage
60S acidic ribosomal protein P0AC [auth BU], BF [auth YU]312Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganismImage
25S ribosomal RNAA [auth BQ], JD [auth YQ]3396Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNAB [auth BR], KD [auth YR]121Saccharomyces cerevisiae
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Entity ID: 3
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNAC [auth BS], LD [auth YS]157Saccharomyces cerevisiae
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Entity ID: 18
MoleculeChainsLengthOrganismImage
18S ribosomal RNAR [auth 2], BC [auth 2b]1800Saccharomyces cerevisiae
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Entity ID: 80
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P-site tRNACF [auth n]76Saccharomyces cerevisiae
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Entity ID: 81
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E-site tRNADF [auth m]75Saccharomyces cerevisiae
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Entity ID: 82
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A/P hybrid tRNAEF [auth nb]76Saccharomyces cerevisiae
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Entity ID: 83
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P/E hybrid tRNAFF [auth mb]77Saccharomyces cerevisiae
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Entity ID: 84
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mRNAGF [auth l]57Saccharomyces cerevisiae
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyFOR1805
German Research FoundationGermanyBE1814/15-1
Japan Society for the Promotion of ScienceJapan26116003

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-16
    Type: Initial release
  • Version 1.1: 2019-03-13
    Changes: Data collection, Database references