› 6r7i

Electron Microscopy
5.9Å resolution

Structural basis of Cullin-2 RING E3 ligase regulation by the COP9 signalosome

Released:
DOI: 10.2210/pdb6r7i/pdb
PDB entry 6r7i coloured by chain, front view.
PDB entry 6r7i coloured by chain, side view.
PDB entry 6r7i coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.
Faull SV, Lau AMC, Martens C, Ahdash Z, Hansen K, Yebenes H, Schmidt C, Beuron F, Cronin NB, Morris EP, Politis A
Nat Commun 10 3814 (2019)
PMID: 31444342
Related structures: EMD-4742

Function and Biology Details

Reactions 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
S-[NEDD8-protein]-yl-[E2 NEDD8-conjugating enzyme]-L-cysteine + [cullin]-L-lysine = [E2 NEDD8-conjugating enzyme]-L-cysteine + N(6)-[NEDD8-protein]-yl-[cullin]-L-lysine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero tridecamer (preferred)
PDBe Complex ID:
PDB-CPX-158230 (preferred)
Entry contents:
13 distinct polypeptide molecules
Macromolecules (13 distinct):
COP9 signalosome complex subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 462 amino acids
Theoretical weight: 52.49 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13098 (Residues: 37-491; Coverage: 93%)
Gene names: COPS1, CSN1, GPS1
Sequence domains:
COP9 signalosome complex subunit 2 Chain: B
Molecule details ›
Chain: B
Length: 443 amino acids
Theoretical weight: 51.66 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P61201 (Residues: 1-443; Coverage: 100%)
Gene names: COPS2, CSN2, TRIP15
Sequence domains: PCI domain
COP9 signalosome complex subunit 3 Chain: C
Molecule details ›
Chain: C
Length: 401 amino acids
Theoretical weight: 45.61 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9UNS2 (Residues: 3-403; Coverage: 95%)
Gene names: COPS3, CSN3
Sequence domains:
COP9 signalosome complex subunit 4 Chain: D
Molecule details ›
Chain: D
Length: 407 amino acids
Theoretical weight: 46.48 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9BT78 (Residues: 1-406; Coverage: 100%)
Gene names: COPS4, CSN4
Sequence domains:
COP9 signalosome complex subunit 5 Chain: E
Molecule details ›
Chain: E
Length: 334 amino acids
Theoretical weight: 37.62 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92905 (Residues: 1-334; Coverage: 100%)
Gene names: COPS5, CSN5, JAB1
Sequence domains:
COP9 signalosome complex subunit 6 Chain: F
Molecule details ›
Chain: F
Length: 327 amino acids
Theoretical weight: 36.2 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q7L5N1 (Residues: 1-327; Coverage: 100%)
Gene names: COPS6, CSN6, HVIP
Sequence domains:
COP9 signalosome complex subunit 7b Chain: G
Molecule details ›
Chain: G
Length: 215 amino acids
Theoretical weight: 23.94 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q9H9Q2 (Residues: 1-215; Coverage: 81%)
Gene names: COPS7B, CSN7B
Sequence domains:
COP9 signalosome complex subunit 8 Chain: H
Molecule details ›
Chain: H
Length: 209 amino acids
Theoretical weight: 23.25 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q99627 (Residues: 1-209; Coverage: 100%)
Gene names: COPS8, CSN8
Sequence domains: CSN8/PSMD8/EIF3K family
NEDD8 Chain: N
Molecule details ›
Chain: N
Length: 78 amino acids
Theoretical weight: 8.88 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
Cullin-2 Chain: O
Molecule details ›
Chain: O
Length: 745 amino acids
Theoretical weight: 87.1 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13617 (Residues: 1-745; Coverage: 100%)
Gene name: CUL2
Sequence domains:
Elongin-B Chain: P
Molecule details ›
Chain: P
Length: 106 amino acids
Theoretical weight: 11.97 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q15370 (Residues: 1-106; Coverage: 90%)
Gene names: ELOB, TCEB2
Sequence domains: Ubiquitin family
Elongin-C Chain: Q
Molecule details ›
Chain: Q
Length: 99 amino acids
Theoretical weight: 11.34 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q03071 (Residues: 1-99; Coverage: 100%)
Gene names: ELC1, YPL046C
Sequence domains: Skp1 family, tetramerisation domain
E3 ubiquitin-protein ligase RBX1, N-terminally processed Chain: R
Molecule details ›
Chain: R
Length: 85 amino acids
Theoretical weight: 10.02 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P62877 (Residues: 19-102; Coverage: 78%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
1 modified residue:
Ligand MSE 3 x MSE

Experiments and Validation Details

Entry percentile scores
Resolution: 5.9Å
Relevant EMDB volumes: EMD-4742
Expression system: Spodoptera frugiperda

Quick links

Citations

13 review citations

Neddylation, an Emerging Mechanism Regulating Cardiac Development and Function.
Li et al. (2020)
12 more

1 mention without citation

Structural basis of Cullin 2 RING E3 ligase regulation by the COP9 signalosome.
Faull et al. (2019)