6R86

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 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:  

  • PubMed Abstract: 
  • Ribosome-associated quality control (RQC) provides a rescue pathway for eukaryotic cells to process faulty proteins after translational stalling of cytoplasmic ribosomes <sup>1-6 </sup>. 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

    Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.,Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Cell Biology, Medical Faculty, University of Munich, Martinsried, Germany. walter.neupert@med.uni-muenchen.de.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany. beckmann@genzentrum.lmu.de.,Department of Cell Biology, Medical Faculty, University of Munich, Martinsried, Germany.,Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan.,Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Martinsried, Germany. walter.neupert@med.uni-muenchen.de.,Gene Center and Center for Integrated Protein Science Munich, Department of Biochemistry, University of Munich, Munich, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1,Protein VMS1
R
475Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: VMS1
Find proteins for Q04311 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q04311
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Eukaryotic translation initiation factor 6
X
224Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: TIF6 (CDC95)
Find proteins for Q12522 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q12522
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L34-A
i
112Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL34A
Find proteins for P87262 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P87262
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L7-A
J
222Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL7A (RPL6A, RPL8A, YL8A)
Find proteins for P05737 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL7A
Go to UniProtKB:  P05737
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L35-A
j
119Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL35A (SOS1)
Find proteins for P0CX84 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL35A
Go to UniProtKB:  P0CX84
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L8-A
K
233Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL8A (MAK7, RPL4A)
Find proteins for P17076 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P17076
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L36-A
k
99Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL36A (RPL39A)
Find proteins for P05745 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL36A
Go to UniProtKB:  P05745
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L9-A
7
191Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL9A (RPL8A, RPL9)
Find proteins for P05738 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05738
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L37-A
l
87Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL37A (RPL35A)
Find proteins for P49166 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL37A
Go to UniProtKB:  P49166
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L11-B
M
169Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL11B (RP39B, RPL16B)
Find proteins for Q3E757 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E757
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L38
m
77Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL38
Find proteins for P49167 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL38
Go to UniProtKB:  P49167
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L13-A
N
193Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL13A
Find proteins for Q12690 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL13A
Go to UniProtKB:  Q12690
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L39
n
50Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL39 (RPL46, SPB2)
Find proteins for P04650 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL39
Go to UniProtKB:  P04650
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L14-A
O
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL14A
Find proteins for P36105 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P36105
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin-60S ribosomal protein L40
o
52Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L15-A
p
203Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL15A (RPL10A, RPL13A, YL10A)
Find proteins for P05748 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05748
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L16-A
Q
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL16A (RPL13, RPL21A)
Find proteins for P26784 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P26784
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L17-A
5
183Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL17A (RPL17, RPL20A)
Find proteins for P05740 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05740
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L18-A
S
185Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL18A (RP28A)
Find proteins for P0CX49 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL18A
Go to UniProtKB:  P0CX49
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L10
s
220Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL10 (GRC5, QSR1)
Find proteins for P41805 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL10
Go to UniProtKB:  P41805
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L19-A
T
152Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL19A (RPL23A, YL14A)
Find proteins for P0CX82 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX82
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L20-A
U
172Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL20A (RPL18A, RPL18A2)
Find proteins for P0CX23 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX23
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L21-A
V
159Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL21A (URP1)
Find proteins for Q02753 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02753
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L22-A
W
100Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL22A
Find proteins for P05749 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05749
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L12-A
P
155Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL12A (RPL15B)
Find proteins for P0CX53 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX53
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
60S acidic ribosomal protein P0
r
197Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPP0 (L10E, RPA0, RPL10E, RPLA0)
Find proteins for P05317 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05317
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L23-A
x
136Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL23A (RPL17A, RPL17AA)
Find proteins for P0CX41 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL23A
Go to UniProtKB:  P0CX41
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L24-A
Y
62Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL24A (RP29, RPL30A)
Find proteins for P04449 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04449
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L25
Z
121Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL25
Find proteins for P04456 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P04456
Entity ID: 32
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L26-A
a
126Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL26A (RPL26, RPL33A)
Find proteins for P05743 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05743
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L27-A
b
135Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL27A (RPL27)
Find proteins for P0C2H6 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL27A
Go to UniProtKB:  P0C2H6
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L42-A
C
105Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL42A (RPL41A, SCL41A)
Find proteins for P0CX27 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX27
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L28
c
148Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL28 (CYH2)
Find proteins for P02406 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL28
Go to UniProtKB:  P02406
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L43-A
D
91Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL43A
Find proteins for P0CX25 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX25
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L29
d
58Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL29 (YL43)
Find proteins for P05747 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL29
Go to UniProtKB:  P05747
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L2-A
E
252Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL2A (RPL5B)
Find proteins for P0CX45 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX45
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L30
e
97Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL30 (RPL32)
Find proteins for P14120 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL30
Go to UniProtKB:  P14120
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L3
F
386Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL3 (MAK8, TCM1)
Find proteins for P14126 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL3
Go to UniProtKB:  P14126
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L31-A
f
109Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL31A (RPL34, RPL34A)
Find proteins for P0C2H8 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0C2H8
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L4-A
G
361Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL4A (RPL2, RPL2A)
Find proteins for P10664 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P10664
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L32
g
127Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL32
Find proteins for P38061 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL32
Go to UniProtKB:  P38061
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L5
H
296Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL5 (RPL1, RPL1A)
Find proteins for P26321 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to Gene View: RPL5
Go to UniProtKB:  P26321
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L33-A
h
106Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL33A (RPL37A)
Find proteins for P05744 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P05744
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L6-A
I
175Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL6A (RPL17A, YL16A)
Find proteins for Q02326 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q02326
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
60S ribosomal protein L1-A
L
204Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL1A (SSM1, SSM1A)
Find proteins for P0CX43 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CX43
Entity ID: 28
MoleculeChainsLengthOrganism
5S ribosomal RNA3121Saccharomyces cerevisiae
Entity ID: 30
MoleculeChainsLengthOrganism
5.8S ribosomal RNA4158Saccharomyces cerevisiae
Entity ID: 48
MoleculeChainsLengthOrganism
25S ribosomal RNA13260Saccharomyces cerevisiae
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
R
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
R
L-PEPTIDE LINKINGC4 H9 N O2

--

MSE
Query on MSE
R
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.4 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



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: 2019-07-31
    Type: Initial release