› 6r87

Electron Microscopy
3.4Å resolution

Yeast Vms1 (Q295L)-60S ribosomal subunit complex (pre-state without Arb1)

Released:
DOI: 10.2210/pdb6r87/pdb
PDB entry 6r87 coloured by chain, front view.
PDB entry 6r87 coloured by chain, side view.
PDB entry 6r87 coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
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 FU, Inada T, Neupert W, Beckmann R
Nature 570 538-542 (2019)
PMID: 31189955
Related structures: EMD-4753

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero 49-mer (preferred)
PDBe Complex ID:
PDB-CPX-135765 (preferred)
Entry contents:
45 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (49 distinct):
tRNA endonuclease VMS1 Chain: R
Molecule details ›
Chain: R
Length: 475 amino acids
Theoretical weight: 53.69 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q04311 (Residues: 13-529; Coverage: 73%)
Gene names: VMS1, YDR049W
Sequence domains: Bacteroidetes VLRF1 release factor
Eukaryotic translation initiation factor 6 Chain: X
Molecule details ›
Chain: X
Length: 224 amino acids
Theoretical weight: 24.16 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12522 (Residues: 1-224; Coverage: 91%)
Gene names: CDC95, LPZ15C, TIF6, YPR016C
Sequence domains: eIF-6 family
Large ribosomal subunit protein eL34A Chain: i
Molecule details ›
Chain: i
Length: 112 amino acids
Theoretical weight: 12.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P87262 (Residues: 2-113; Coverage: 93%)
Gene names: RPL34A, YER056BC, YER056C-A
Sequence domains: Ribosomal protein L34e
Large ribosomal subunit protein uL30A Chain: J
Molecule details ›
Chain: J
Length: 222 amino acids
Theoretical weight: 25.24 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05737 (Residues: 23-244; Coverage: 91%)
Gene names: RPL6A, RPL7A, RPL8A, YGL076C, YL8A
Sequence domains:
Large ribosomal subunit protein uL29A Chain: j
Molecule details ›
Chain: j
Length: 119 amino acids
Theoretical weight: 13.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX84 (Residues: 2-120; Coverage: 99%)
Gene names: D1249, RPL35A, SOS1, YDL191W
Sequence domains: Ribosomal L29 protein
Large ribosomal subunit protein eL8A Chain: K
Molecule details ›
Chain: K
Length: 233 amino acids
Theoretical weight: 25.81 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P17076 (Residues: 24-256; Coverage: 91%)
Gene names: MAK7, RPL4A, RPL8A, YHL033C
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein eL36A Chain: k
Molecule details ›
Chain: k
Length: 99 amino acids
Theoretical weight: 11.02 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05745 (Residues: 2-100; Coverage: 99%)
Gene names: RPL36A, RPL39A, YM9646.06, YMR194W
Sequence domains: Ribosomal protein L36e
Large ribosomal subunit protein uL6A Chain: 7
Molecule details ›
Chain: 7
Length: 191 amino acids
Theoretical weight: 21.61 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05738 (Residues: 1-191; Coverage: 100%)
Gene names: RPL8A, RPL9, RPL9A, YGL147C
Sequence domains: Ribosomal protein L6
Large ribosomal subunit protein eL37A Chain: l
Molecule details ›
Chain: l
Length: 87 amino acids
Theoretical weight: 9.75 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49166 (Residues: 2-88; Coverage: 99%)
Gene names: L9470.6, RPL35A, RPL37A, YLR185W
Sequence domains: Ribosomal protein L37e
Large ribosomal subunit protein uL5B Chain: M
Molecule details ›
Chain: M
Length: 169 amino acids
Theoretical weight: 19.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q3E757 (Residues: 6-174; Coverage: 97%)
Gene names: RP39B, RPL11B, RPL16B, YGR085C
Sequence domains:
Large ribosomal subunit protein eL38 Chain: m
Molecule details ›
Chain: m
Length: 77 amino acids
Theoretical weight: 8.71 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P49167 (Residues: 2-78; Coverage: 99%)
Gene names: L8543.2, RPL38, YLR325C
Sequence domains: Ribosomal L38e protein family
Large ribosomal subunit protein eL13A Chain: N
Molecule details ›
Chain: N
Length: 193 amino acids
Theoretical weight: 21.89 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q12690 (Residues: 2-194; Coverage: 97%)
Gene names: RPL13A, YDL082W
Sequence domains: Ribosomal protein L13e
Large ribosomal subunit protein eL39 Chain: n
Molecule details ›
Chain: n
Length: 50 amino acids
Theoretical weight: 6.23 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04650 (Residues: 2-51; Coverage: 98%)
Gene names: J0360, RPL39, RPL46, SPB2, YJL189W
Sequence domains: Ribosomal L39 protein
Large ribosomal subunit protein eL14A Chain: O
Molecule details ›
Chain: O
Length: 136 amino acids
Theoretical weight: 14.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P36105 (Residues: 3-138; Coverage: 99%)
Gene names: RPL14A, YKL006W, YKL153
Sequence domains:
Large ribosomal subunit protein eL40A Chain: o
Molecule details ›
Chain: o
Length: 52 amino acids
Theoretical weight: 6.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CH08 (Residues: 77-128; Coverage: 41%)
Gene names: RPL40A, UBI1, YIL148W
Sequence domains: Ribosomal L40e family
Large ribosomal subunit protein eL15A Chain: p
Molecule details ›
Chain: p
Length: 203 amino acids
Theoretical weight: 24.35 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05748 (Residues: 2-204; Coverage: 100%)
Gene names: RPL10A, RPL13A, RPL15A, YL10A, YLR029C
Sequence domains: Ribosomal L15
Large ribosomal subunit protein uL13A Chain: Q
Molecule details ›
Chain: Q
Length: 197 amino acids
Theoretical weight: 22.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26784 (Residues: 3-199; Coverage: 99%)
Gene names: RPL13, RPL16A, RPL21A, YIL133C
Sequence domains: Ribosomal protein L13
Large ribosomal subunit protein uL22A Chain: 5
Molecule details ›
Chain: 5
Length: 183 amino acids
Theoretical weight: 20.46 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05740 (Residues: 2-184; Coverage: 100%)
Gene names: RPL17, RPL17A, RPL20A, YKL180W
Sequence domains: Ribosomal protein L22p/L17e
Large ribosomal subunit protein eL18A Chain: S
Molecule details ›
Chain: S
Length: 185 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX49 (Residues: 2-186; Coverage: 100%)
Gene names: RP28A, RPL18A, YOL120C
Sequence domains: Ribosomal protein 60S L18 and 50S L18e
Large ribosomal subunit protein uL16 Chain: s
Molecule details ›
Chain: s
Length: 220 amino acids
Theoretical weight: 25.28 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P41805 (Residues: 2-221; Coverage: 100%)
Gene names: GRC5, QSR1, RPL10, YLR075W
Sequence domains: Ribosomal protein L16p/L10e
Large ribosomal subunit protein eL19A Chain: T
Molecule details ›
Chain: T
Length: 152 amino acids
Theoretical weight: 17.45 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX82 (Residues: 2-153; Coverage: 80%)
Gene names: RPL19A, RPL23A, YBR084BC, YBR084C-A, YL14A
Sequence domains: Ribosomal protein L19e
Large ribosomal subunit protein eL20A Chain: U
Molecule details ›
Chain: U
Length: 172 amino acids
Theoretical weight: 20.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX23 (Residues: 1-172; Coverage: 100%)
Gene names: RPL18A, RPL18A2, RPL20A, YM9408.04C, YMR242C
Sequence domains: Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A
Large ribosomal subunit protein eL21A Chain: V
Molecule details ›
Chain: V
Length: 159 amino acids
Theoretical weight: 18.15 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02753 (Residues: 2-160; Coverage: 99%)
Gene names: RPL21A, URP1, YBR1401, YBR191W
Sequence domains: Ribosomal protein L21e
Large ribosomal subunit protein eL22A Chain: W
Molecule details ›
Chain: W
Length: 100 amino acids
Theoretical weight: 11.26 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05749 (Residues: 9-108; Coverage: 83%)
Gene names: L2168, RPL22A, YLR061W
Sequence domains: Ribosomal L22e protein family
Large ribosomal subunit protein uL11A Chain: P
Molecule details ›
Chain: P
Length: 155 amino acids
Theoretical weight: 16.68 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX53 (Residues: 9-163; Coverage: 94%)
Gene names: RPL12A, RPL15B, YEL054C
Sequence domains:
Large ribosomal subunit protein uL10 Chain: r
Molecule details ›
Chain: r
Length: 197 amino acids
Theoretical weight: 21.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05317 (Residues: 3-199; Coverage: 63%)
Gene names: L10E, L8300.8, RPA0, RPL10E, RPLA0, RPP0, YLR340W
Sequence domains:
Large ribosomal subunit protein uL14A Chain: x
Molecule details ›
Chain: x
Length: 136 amino acids
Theoretical weight: 14.36 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX41 (Residues: 2-137; Coverage: 99%)
Gene names: RPL17A, RPL17AA, RPL23A, YBL0713, YBL087C
Sequence domains: Ribosomal protein L14p/L23e
Large ribosomal subunit protein eL24A Chain: Y
Molecule details ›
Chain: Y
Length: 62 amino acids
Theoretical weight: 7.27 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04449 (Residues: 1-62; Coverage: 40%)
Gene names: RP29, RPL24A, RPL30A, YGL031C
Sequence domains: Ribosomal protein L24e
Large ribosomal subunit protein uL23 Chain: Z
Molecule details ›
Chain: Z
Length: 121 amino acids
Theoretical weight: 13.77 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P04456 (Residues: 22-142; Coverage: 85%)
Gene names: RPL25, YOL127W
Sequence domains:
Large ribosomal subunit protein uL24A Chain: a
Molecule details ›
Chain: a
Length: 126 amino acids
Theoretical weight: 14.13 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05743 (Residues: 2-127; Coverage: 99%)
Gene names: L8300.4, RPL26, RPL26A, RPL33A, YLR344W
Sequence domains:
Large ribosomal subunit protein eL27A Chain: b
Molecule details ›
Chain: b
Length: 135 amino acids
Theoretical weight: 15.44 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H6 (Residues: 2-136; Coverage: 99%)
Gene names: RPL27, RPL27A, YHR010W
Sequence domains: Ribosomal L27e protein family
Large ribosomal subunit protein eL42A Chain: C
Molecule details ›
Chain: C
Length: 105 amino acids
Theoretical weight: 12.12 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX27 (Residues: 2-106; Coverage: 99%)
Gene names: N1722, RPL41A, RPL42A, SCL41A, YNL162W
Sequence domains: Ribosomal protein L44
Large ribosomal subunit protein uL15 Chain: c
Molecule details ›
Chain: c
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P02406 (Residues: 2-149; Coverage: 99%)
Gene names: CYH2, RPL28, YGL103W
Sequence domains: Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A
Large ribosomal subunit protein eL43A Chain: D
Molecule details ›
Chain: D
Length: 91 amino acids
Theoretical weight: 9.98 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX25 (Residues: 2-92; Coverage: 99%)
Gene names: RPL43A, YP9499.02, YPR043W
Sequence domains: Ribosomal L37ae protein family
Large ribosomal subunit protein eL29 Chain: d
Molecule details ›
Chain: d
Length: 58 amino acids
Theoretical weight: 6.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05747 (Residues: 2-59; Coverage: 98%)
Gene names: RPL29, YFR032BW, YFR032C-A, YL43
Sequence domains: Ribosomal L29e protein family
Large ribosomal subunit protein uL2A Chain: E
Molecule details ›
Chain: E
Length: 252 amino acids
Theoretical weight: 27.22 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX45 (Residues: 2-253; Coverage: 99%)
Gene names: RPL2A, RPL5B, YFR031BC, YFR031C-A
Sequence domains:
Large ribosomal subunit protein eL30 Chain: e
Molecule details ›
Chain: e
Length: 97 amino acids
Theoretical weight: 10.56 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14120 (Residues: 9-105; Coverage: 92%)
Gene names: RPL30, RPL32, YGL030W
Sequence domains: Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
Large ribosomal subunit protein uL3 Chain: F
Molecule details ›
Chain: F
Length: 386 amino acids
Theoretical weight: 43.72 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P14126 (Residues: 2-387; Coverage: 100%)
Gene names: MAK8, RPL3, TCM1, YOR063W, YOR29-14
Sequence domains: Ribosomal protein L3
Large ribosomal subunit protein eL31A Chain: f
Molecule details ›
Chain: f
Length: 109 amino acids
Theoretical weight: 12.65 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0C2H8 (Residues: 4-112; Coverage: 97%)
Gene names: D2478, RPL31A, RPL34, RPL34A, YDL075W
Sequence domains: Ribosomal protein L31e
Large ribosomal subunit protein uL4A Chain: G
Molecule details ›
Chain: G
Length: 361 amino acids
Theoretical weight: 39.03 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P10664 (Residues: 2-362; Coverage: 100%)
Gene names: RPL2, RPL2A, RPL4A, YBR0315, YBR031W
Sequence domains:
Large ribosomal subunit protein eL32 Chain: g
Molecule details ›
Chain: g
Length: 127 amino acids
Theoretical weight: 14.48 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P38061 (Residues: 2-128; Coverage: 98%)
Gene names: RPL32, YBL0838, YBL092W
Sequence domains: Ribosomal protein L32
Large ribosomal subunit protein uL18 Chain: H
Molecule details ›
Chain: H
Length: 296 amino acids
Theoretical weight: 33.63 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P26321 (Residues: 2-297; Coverage: 100%)
Gene names: LPI14W, RPL1, RPL1A, RPL5, YPL131W
Sequence domains:
Large ribosomal subunit protein eL33A Chain: h
Molecule details ›
Chain: h
Length: 106 amino acids
Theoretical weight: 12.05 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P05744 (Residues: 2-107; Coverage: 99%)
Gene names: LPI4W, P2625, RPL33A, RPL37A, YPL143W
Sequence domains: Ribosomal protein L35Ae
Large ribosomal subunit protein eL6A Chain: I
Molecule details ›
Chain: I
Length: 175 amino acids
Theoretical weight: 19.87 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: Q02326 (Residues: 2-176; Coverage: 99%)
Gene names: RPL17A, RPL6A, YL16A, YML073C
Sequence domains: Ribosomal protein L6e
Large ribosomal subunit protein uL1A Chain: L
Molecule details ›
Chain: L
Length: 204 amino acids
Theoretical weight: 22.97 KDa
Source organism: Saccharomyces cerevisiae
UniProt:
  • Canonical: P0CX43 (Residues: 13-216; Coverage: 94%)
Gene names: RPL1A, SSM1, SSM1A, YPL220W
Sequence domains: Ribosomal protein L1p/L10e family
5S ribosomal RNA Chain: 3
Molecule details ›
Chain: 3
Length: 121 nucleotides
Theoretical weight: 38.95 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 4
Molecule details ›
Chain: 4
Length: 158 nucleotides
Theoretical weight: 50.68 KDa
Sequence domains: 5.8S ribosomal RNA
tRNA-Ala Chain: B
Molecule details ›
Chain: B
Length: 76 nucleotides
Theoretical weight: 24.5 KDa
Sequence domains: tRNA
25S ribosomal RNA Chain: 1
Molecule details ›
Chain: 1
Length: 3316 nucleotides
Theoretical weight: 1071.85 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA

Ligands and Environments

1 bound ligand:
Ligand ZN 1 x ZN
1 modified residue:
Ligand MSE 1 x MSE

Experiments and Validation Details

Entry percentile scores
Resolution: 3.4Å
Relevant EMDB volumes: EMD-4753
Expression system: Saccharomyces cerevisiae

Quick links

Citations

17 review citations

Ribosomal stress-surveillance: three pathways is a magic number.
Vind et al. (2020)
16 more