6R84

Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state with Arb1)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and function of Vms1 and Arb1 in RQC and mitochondrial proteome homeostasis.

Su, T.Izawa, T.Thoms, M.Yamashita, Y.Cheng, J.Berninghausen, O.Hartl, F.U.Inada, T.Neupert, W.Beckmann, R.

(2019) Nature 570: 538-542

  • DOI: 10.1038/s41586-019-1307-z
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes 1-6 . After dissociation of ribosomes, the stalled tRNA-bound peptide ...

    Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes 1-6 . After dissociation of ribosomes, the stalled tRNA-bound peptide remains associated with the 60S subunit and extended by Rqc2 by addition of C-terminal alanyl and threonyl residues (CAT tails) 7-9 , whereas Vms1 catalyses cleavage and release of the peptidyl-tRNA before or after addition of CAT tails 10-12 . In doing so, Vms1 counteracts CAT-tailing of nuclear-encoded mitochondrial proteins that otherwise drive aggregation and compromise mitochondrial and cellular homeostasis 13 . Here we present structural and functional insights into the interaction of Saccharomyces cerevisiae Vms1 with 60S subunits in pre- and post-peptidyl-tRNA cleavage states. Vms1 binds to 60S subunits with its Vms1-like release factor 1 (VLRF1), zinc finger and ankyrin domains. VLRF1 overlaps with the Rqc2 A-tRNA position and interacts with the ribosomal A-site, projecting its catalytic GSQ motif towards the CCA end of the tRNA, its Y285 residue dislodging the tRNA A73 for nucleolytic cleavage. Moreover, in the pre-state, we found the ABCF-type ATPase Arb1 in the ribosomal E-site, which stabilizes the delocalized A73 of the peptidyl-tRNA and stimulates Vms1-dependent tRNA cleavage. Our structural analysis provides mechanistic insights into the interplay of the RQC factors Vms1, Rqc2 and Arb1 and their role in the protection of mitochondria from the aggregation of toxic proteins.


    Organizational Affiliation

    Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter ATP-binding protein ARB1A519Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P40024 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-Al87Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-BM169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38m77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-AN193Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39n50Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-AO136Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL14AYKL006WYKL153
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40o52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-Ap203Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-AQ197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A5183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Protein VMS1,Vms1,Protein VMS1,Vms1R433Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VMS1YDR049W
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Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-AS185Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10s220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-AT152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-AU172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-AV159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-AW100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12-AP155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0r197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-Ax136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6X224Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-AY62Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25Z121Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-Aa126Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-Ab135Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-AC105Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28c148Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-AD91Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29d58Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-Ai112Saccharomyces cerevisiaeMutation(s): 0 
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-AE252Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30e97Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3F386Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-Af109Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-AG361Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32g127Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5H296Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-Ah106Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-AI175Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1-AL204Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-AJ222Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-Aj119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-AK233Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-Ak99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A7191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
MoleculeChainsLengthOrganism
5S rRNA3121Saccharomyces cerevisiae

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Entity ID: 31
MoleculeChainsLengthOrganism
5.8S rRNA4158Saccharomyces cerevisiae

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Entity ID: 34
MoleculeChainsLengthOrganism
tRNA-AlaB76Saccharomyces cerevisiae

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Entity ID: 50
MoleculeChainsLengthOrganism
25S rRNA13316Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
RL-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanyNE 101/28-1
German Research FoundationGermanyGRK1721
German Research FoundationGermanythe Graduate School of Quantitative Biosciences Munich (QBM)

Revision History 

  • Version 1.0: 2019-06-26
    Type: Initial release
  • Version 1.1: 2019-07-03
    Changes: Data collection, Structure summary
  • Version 1.2: 2019-07-10
    Changes: Data collection, Database references