3j92

Electron Microscopy
3.6Å resolution

Structure and assembly pathway of the ribosome quality control complex

Released:
Related structures: EMD-2832

Function and Biology Details

Reaction catalysed:
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero 55-mer (preferred)
PDBe Complex ID:
PDB-CPX-130012 (preferred)
Entry contents:
47 distinct polypeptide molecules
4 distinct RNA molecules
Macromolecules (51 distinct):
uL2 Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.09 KDa
Source organism: Oryctolagus cuniculus
uL3 Chain: B
Molecule details ›
Chain: B
Length: 395 amino acids
Theoretical weight: 44.89 KDa
Source organism: Oryctolagus cuniculus
uL4 Chain: C
Molecule details ›
Chain: C
Length: 368 amino acids
Theoretical weight: 41.77 KDa
Source organism: Oryctolagus cuniculus
uL18 Chain: D
Molecule details ›
Chain: D
Length: 297 amino acids
Theoretical weight: 34.42 KDa
Source organism: Oryctolagus cuniculus
eL6 Chain: E
Molecule details ›
Chain: E
Length: 284 amino acids
Theoretical weight: 32.3 KDa
Source organism: Oryctolagus cuniculus
eL30 Chain: F
Molecule details ›
Chain: F
Length: 250 amino acids
Theoretical weight: 29.52 KDa
Source organism: Oryctolagus cuniculus
eL8 Chain: G
Molecule details ›
Chain: G
Length: 266 amino acids
Theoretical weight: 30.17 KDa
Source organism: Oryctolagus cuniculus
uL6 Chain: H
Molecule details ›
Chain: H
Length: 192 amino acids
Theoretical weight: 21.9 KDa
Source organism: Oryctolagus cuniculus
uL16 Chain: I
Molecule details ›
Chain: I
Length: 214 amino acids
Theoretical weight: 24.6 KDa
Source organism: Oryctolagus cuniculus
uL5 Chain: J
Molecule details ›
Chain: J
Length: 178 amino acids
Theoretical weight: 20.25 KDa
Source organism: Oryctolagus cuniculus
eL13 Chain: L
Molecule details ›
Chain: L
Length: 211 amino acids
Theoretical weight: 24.37 KDa
Source organism: Oryctolagus cuniculus
eL14 Chain: M
Molecule details ›
Chain: M
Length: 213 amino acids
Theoretical weight: 23.38 KDa
Source organism: Oryctolagus cuniculus
eL15 Chain: N
Molecule details ›
Chain: N
Length: 204 amino acids
Theoretical weight: 24.21 KDa
Source organism: Oryctolagus cuniculus
uL13 Chain: O
Molecule details ›
Chain: O
Length: 204 amino acids
Theoretical weight: 23.77 KDa
Source organism: Oryctolagus cuniculus
uL22 Chain: P
Molecule details ›
Chain: P
Length: 184 amino acids
Theoretical weight: 21.44 KDa
Source organism: Oryctolagus cuniculus
eL18 Chain: Q
Molecule details ›
Chain: Q
Length: 188 amino acids
Theoretical weight: 21.59 KDa
Source organism: Oryctolagus cuniculus
eL19 Chain: R
Molecule details ›
Chain: R
Length: 196 amino acids
Theoretical weight: 23.57 KDa
Source organism: Oryctolagus cuniculus
eL20 Chain: S
Molecule details ›
Chain: S
Length: 224 amino acids
Theoretical weight: 26.1 KDa
Source organism: Oryctolagus cuniculus
eL21 Chain: T
Molecule details ›
Chain: T
Length: 160 amino acids
Theoretical weight: 18.61 KDa
Source organism: Oryctolagus cuniculus
eL22 Chain: U
Molecule details ›
Chain: U
Length: 128 amino acids
Theoretical weight: 14.78 KDa
Source organism: Oryctolagus cuniculus
uL14 Chain: V
Molecule details ›
Chain: V
Length: 140 amino acids
Theoretical weight: 14.89 KDa
Source organism: Oryctolagus cuniculus
eL24 Chain: W
Molecule details ›
Chain: W
Length: 157 amino acids
Theoretical weight: 17.83 KDa
Source organism: Oryctolagus cuniculus
uL23 Chain: X
Molecule details ›
Chain: X
Length: 156 amino acids
Theoretical weight: 17.74 KDa
Source organism: Oryctolagus cuniculus
uL24 Chain: Y
Molecule details ›
Chain: Y
Length: 145 amino acids
Theoretical weight: 17.3 KDa
Source organism: Oryctolagus cuniculus
eL27 Chain: Z
Molecule details ›
Chain: Z
Length: 136 amino acids
Theoretical weight: 15.84 KDa
Source organism: Oryctolagus cuniculus
uL15 Chain: a
Molecule details ›
Chain: a
Length: 148 amino acids
Theoretical weight: 16.63 KDa
Source organism: Oryctolagus cuniculus
eL29 Chain: b
Molecule details ›
Chain: b
Length: 160 amino acids
Theoretical weight: 17.55 KDa
Source organism: Oryctolagus cuniculus
eL30 Chain: c
Molecule details ›
Chain: c
Length: 115 amino acids
Theoretical weight: 12.81 KDa
Source organism: Oryctolagus cuniculus
eL31 Chain: d
Molecule details ›
Chain: d
Length: 125 amino acids
Theoretical weight: 14.49 KDa
Source organism: Oryctolagus cuniculus
eL32 Chain: e
Molecule details ›
Chain: e
Length: 135 amino acids
Theoretical weight: 15.9 KDa
Source organism: Oryctolagus cuniculus
eL33 Chain: f
Molecule details ›
Chain: f
Length: 110 amino acids
Theoretical weight: 12.56 KDa
Source organism: Oryctolagus cuniculus
eL34 Chain: g
Molecule details ›
Chain: g
Length: 117 amino acids
Theoretical weight: 13.33 KDa
Source organism: Oryctolagus cuniculus
uL29 Chain: h
Molecule details ›
Chain: h
Length: 123 amino acids
Theoretical weight: 14.59 KDa
Source organism: Oryctolagus cuniculus
eL36 Chain: i
Molecule details ›
Chain: i
Length: 105 amino acids
Theoretical weight: 12.29 KDa
Source organism: Oryctolagus cuniculus
eL37 Chain: j
Molecule details ›
Chain: j
Length: 97 amino acids
Theoretical weight: 11.12 KDa
Source organism: Oryctolagus cuniculus
eL38 Chain: k
Molecule details ›
Chain: k
Length: 70 amino acids
Theoretical weight: 8.24 KDa
Source organism: Oryctolagus cuniculus
eL39 Chain: l
Molecule details ›
Chain: l
Length: 51 amino acids
Theoretical weight: 6.43 KDa
Source organism: Oryctolagus cuniculus
eL40 Chain: m
Molecule details ›
Chain: m
Length: 128 amino acids
Theoretical weight: 14.76 KDa
Source organism: Oryctolagus cuniculus
eL42 Chain: o
Molecule details ›
Chain: o
Length: 106 amino acids
Theoretical weight: 12.48 KDa
Source organism: Oryctolagus cuniculus
eL43 Chain: p
Molecule details ›
Chain: p
Length: 92 amino acids
Theoretical weight: 10.3 KDa
Source organism: Oryctolagus cuniculus
eL28 Chain: r
Molecule details ›
Chain: r
Length: 137 amino acids
Theoretical weight: 15.77 KDa
Source organism: Oryctolagus cuniculus
uL10 Chain: s
Molecule details ›
Chain: s
Length: 317 amino acids
Theoretical weight: 34.31 KDa
Source organism: Oryctolagus cuniculus
uL11 Chain: t
Molecule details ›
Chain: t
Length: 165 amino acids
Theoretical weight: 17.85 KDa
Source organism: Oryctolagus cuniculus
Ribosome quality control complex subunit NEMF Chains: u, v
Molecule details ›
Chains: u, v
Length: 501 amino acids
Theoretical weight: 57.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O60524 (Residues: 1-501; Coverage: 47%)
Gene names: NEMF, SDCCAG1
Sequence domains: NFACT N-terminal and middle domains
E3 ubiquitin-protein ligase listerin Chains: 0, w, z
Molecule details ›
Chains: 0, w, z
Length: 1766 amino acids
Theoretical weight: 200.78 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
UniProt:
  • Canonical: O94822 (Residues: 1-1766; Coverage: 100%)
Gene names: C21orf10, C21orf98, HSPC087, KIAA0714, LTN1, RNF160, ZNF294
Listerin Chains: x, y
Molecule details ›
Chains: x, y
Length: 218 amino acids
Theoretical weight: 18.57 KDa
Source organism: Homo sapiens
Expression system: Homo sapiens
nascent chain Chain: 1
Molecule details ›
Chain: 1
Length: 104 amino acids
Theoretical weight: 10.9 KDa
Source organism: Oryctolagus cuniculus
tRNA Chain: 2
Molecule details ›
Chain: 2
Length: 77 nucleotides
Theoretical weight: 24.82 KDa
Sequence domains: tRNA
28S ribosomal RNA Chain: 5
Molecule details ›
Chain: 5
Length: 3664 nucleotides
Theoretical weight: 1187.23 KDa
Sequence domains: Eukaryotic large subunit ribosomal RNA
5S ribosomal RNA Chain: 7
Molecule details ›
Chain: 7
Length: 120 nucleotides
Theoretical weight: 38.69 KDa
Sequence domains: 5S ribosomal RNA
5.8S ribosomal RNA Chain: 8
Molecule details ›
Chain: 8
Length: 156 nucleotides
Theoretical weight: 50.14 KDa
Sequence domains: 5.8S ribosomal RNA

Ligands and Environments

2 bound ligands:
1 modified residue:

Experiments and Validation Details

Entry percentile scores
Resolution: 3.6Å
Relevant EMDB volumes: EMD-2832
Expression system: Homo sapiens