6S47

Saccharomyces cerevisiae 80S ribosome bound with ABCF protein New1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 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

A role for the Saccharomyces cerevisiae ABCF protein New1 in translation termination/recycling.

Kasari, V.Pochopien, A.A.Margus, T.Murina, V.Turnbull, K.Zhou, Y.Nissan, T.Graf, M.Novacek, J.Atkinson, G.C.Johansson, M.J.O.Wilson, D.N.Hauryliuk, V.

(2019) Nucleic Acids Res 47: 8807-8820

  • DOI: 10.1093/nar/gkz600
  • Primary Citation of Related Structures:  
    6S47

  • PubMed Abstract: 
  • Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes ...

    Translation is controlled by numerous accessory proteins and translation factors. In the yeast Saccharomyces cerevisiae, translation elongation requires an essential elongation factor, the ABCF ATPase eEF3. A closely related protein, New1, is encoded by a non-essential gene with cold sensitivity and ribosome assembly defect knock-out phenotypes. Since the exact molecular function of New1 is unknown, it is unclear if the ribosome assembly defect is direct, i.e. New1 is a bona fide assembly factor, or indirect, for instance due to a defect in protein synthesis. To investigate this, we employed yeast genetics, cryo-electron microscopy (cryo-EM) and ribosome profiling (Ribo-Seq) to interrogate the molecular function of New1. Overexpression of New1 rescues the inviability of a yeast strain lacking the otherwise strictly essential translation factor eEF3. The structure of the ATPase-deficient (EQ2) New1 mutant locked on the 80S ribosome reveals that New1 binds analogously to the ribosome as eEF3. Finally, Ribo-Seq analysis revealed that loss of New1 leads to ribosome queuing upstream of 3'-terminal lysine and arginine codons, including those genes encoding proteins of the cytoplasmic translational machinery. Our results suggest that New1 is a translation factor that fine-tunes the efficiency of translation termination or ribosome recycling.


    Organizational Affiliation

    University of Tartu, Institute of Technology, 50411 Tartu, Estonia.



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Entity ID: 4
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60S ribosomal protein L2-AD [auth AD]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3E [auth AE]386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L4-AF [auth AF]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5G [auth AG]296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-AH [auth AH]175Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L7-AI [auth AI]243Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L8-AJ [auth AJ]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L9-AK [auth AK]191Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10L [auth AL]220Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BM [auth AM]169Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L13-AN [auth AN]198Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AO [auth AO]137Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L15-AP [auth AP]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AQ [auth AQ]198Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L17-AR [auth AR]183Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L18-AS [auth AS]185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L19-AT [auth AT]188Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L20-AU [auth AU]172Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L21-AV [auth AV]159Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L22-AW [auth AW]120Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L23-AX [auth AX]136Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L24-AY [auth AY]155Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25Z [auth AZ]141Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AAA [auth Aa]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-ABA [auth Ab]135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28CA [auth Ac]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29DA [auth Ad]58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30EA [auth Ae]104Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AFA [auth Af]112Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32GA [auth Ag]129Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-AHA [auth Ah]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L34-AIA [auth Ai]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-AJA [auth Aj]119Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AKA [auth Ak]99Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L37-ALA [auth Al]87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L38MA [auth Am]77Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39NA [auth An]50Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40OA [auth Ao]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L41-BPA [auth Ap]25Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-AQA [auth Aq]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-ARA [auth Ar]91Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S0-ATA [auth BB]251Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S1-AUA [auth BC]254Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S2VA [auth BD]253Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S3WA [auth BE]239Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S4-AXA [auth BF]260Saccharomyces cerevisiaeMutation(s): 0 
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Rps5pYA [auth BG]224Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S6-AZA [auth BH]236Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S7-AAB [auth BI]189Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S8-ABB [auth BJ]199Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S9-ACB [auth BK]196Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S10-ADB [auth BL]105Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S11-AEB [auth BM]155Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S12FB [auth BN]142Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S13GB [auth BO]150Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S14-AHB [auth BP]136Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S15IB [auth BQ]141Saccharomyces cerevisiaeMutation(s): 0 
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40S ribosomal protein S16-AJB [auth BR]142Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 63
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40S ribosomal protein S17-AKB [auth BS]135Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 64
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40S ribosomal protein S18-ALB [auth BT]145Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 65
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40S ribosomal protein S19-AMB [auth BU]143Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 66
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40S ribosomal protein S20NB [auth BV]120Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 67
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40S ribosomal protein S21-AOB [auth BW]87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 68
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40S ribosomal protein S22-APB [auth BX]129Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0C0W1 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 69
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40S ribosomal protein S23-AQB [auth BY]144Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 70
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40S ribosomal protein S24-ARB [auth BZ]134Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 71
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40S ribosomal protein S25-ASB [auth Ba]107Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 72
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40S ribosomal protein S26-BTB [auth Bb]118Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 73
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40S ribosomal protein S27-AUB [auth Bc]81Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 74
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40S ribosomal protein S28-AVB [auth Bd]66Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 75
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40S ribosomal protein S29-AWB [auth Be]55Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 76
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40S ribosomal protein S30-AXB [auth Bf]62Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 77
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Ubiquitin-40S ribosomal protein S31YB [auth Bg]151Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 78
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Guanine nucleotide-binding protein subunit beta-like proteinZB [auth Bh]318Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 79
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[NU+] prion formation protein 1AC [auth Bi]972Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NEW1YPL226WP1445
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Find proteins for Q08972 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 1
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28S ribosomal RNAA [auth AA]3149Saccharomyces cerevisiae
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Entity ID: 2
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5S ribosomal RNAB [auth AB]121Saccharomyces cerevisiae
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Entity ID: 3
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5.8S ribosomal RNAC [auth AC]158Saccharomyces cerevisiae
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Entity ID: 45
MoleculeChainsLengthOrganismImage
18S rRNA (1707-MER)SA [auth BA]1707Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP

Download Ideal Coordinates CCD File 
BC [auth Bi], CC [auth Bi]ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.28 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 FoundationGermanyGrant WI3285/8-1

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-24
    Type: Initial release
  • Version 1.1: 2019-10-23
    Changes: Data collection, Database references