6R86

Yeast Vms1-60S ribosomal subunit complex (post-state)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 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
  • Primary Citation of Related Structures:  
    6R84, 6R86, 6R87

  • 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 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 ...

    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 LengthOrganismDetailsImage
Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1A [auth R]475Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: VMS1YDR049W
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Eukaryotic translation initiation factor 6B [auth X]224Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L34-AC [auth i]112Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 4
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60S ribosomal protein L7-AD [auth J]222Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L35-AE [auth j]119Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 6
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60S ribosomal protein L8-AF [auth K]233Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L36-AG [auth k]99Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 8
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60S ribosomal protein L9-AH [auth 7]191Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 9
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60S ribosomal protein L37-AI [auth l]87Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L11-BJ [auth M]169Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 11
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60S ribosomal protein L38K [auth m]77Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 12
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60S ribosomal protein L13-AL [auth N]193Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L39M [auth n]50Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L14-AN [auth O]136Saccharomyces cerevisiaeMutation(s): 0 
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Ubiquitin-60S ribosomal protein L40O [auth o]52Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 16
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60S ribosomal protein L15-AP [auth p]203Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L16-AQ197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 18
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60S ribosomal protein L17-AR [auth 5]183Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 19
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60S ribosomal protein L18-AS185Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L10T [auth s]220Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 21
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60S ribosomal protein L19-AU [auth T]152Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 22
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60S ribosomal protein L20-AV [auth U]172Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 23
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60S ribosomal protein L21-AW [auth V]159Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 24
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60S ribosomal protein L22-AX [auth W]100Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 25
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60S ribosomal protein L12-AY [auth P]155Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 26
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60S acidic ribosomal protein P0Z [auth r]197Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 27
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60S ribosomal protein L23-AAA [auth x]136Saccharomyces cerevisiaeMutation(s): 0 
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Entity ID: 29
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60S ribosomal protein L24-ACA [auth Y]62Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L25EA [auth Z]121Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L26-AFA [auth a]126Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L27-AGA [auth b]135Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L42-AHA [auth C]105Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L28IA [auth c]148Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L43-AJA [auth D]91Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L29KA [auth d]58Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L2-ALA [auth E]252Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L30MA [auth e]97Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L3NA [auth F]386Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L31-AOA [auth f]109Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L4-APA [auth G]361Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L32QA [auth g]127Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L5RA [auth H]296Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L33-ASA [auth h]106Saccharomyces cerevisiaeMutation(s): 0 
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60S ribosomal protein L6-ATA [auth I]175Saccharomyces cerevisiaeMutation(s): 0 
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UniProt GroupQ02326
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Entity ID: 47
MoleculeChainsSequence LengthOrganismDetailsImage
60S ribosomal protein L1-AUA [auth L]204Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CX43 
Go to UniProtKB:  P0CX43
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UniProt GroupP0CX43
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Entity ID: 28
MoleculeChainsLengthOrganismImage
5S ribosomal RNABA [auth 3]121Saccharomyces cerevisiae
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Entity ID: 30
MoleculeChainsLengthOrganismImage
5.8S ribosomal RNADA [auth 4]158Saccharomyces cerevisiae
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Entity ID: 48
MoleculeChainsLengthOrganismImage
25S ribosomal RNAVA [auth 1]3260Saccharomyces cerevisiae
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Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
WA [auth R]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A [auth R]L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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 FoundationGermanyNE 101/28-1
German Research FoundationGermanyGRK1721
German Research FoundationGermanythe Graduate School of Quantitative Biosciences Munich (QBM)

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-31
    Type: Initial release