› 4d10

X-ray diffraction
3.8Å resolution

Crystal structure of the COP9 signalosome

Released:
DOI: 10.2210/pdb4d10/pdb
PDB entry 4d10 coloured by chain, front view.
PDB entry 4d10 coloured by chain, side view.
PDB entry 4d10 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal structure of the human COP9 signalosome.
Lingaraju GM, Bunker RD, Cavadini S, Hess D, Hassiepen U, Renatus M, Fischer ES, Thomä NH
Nature 512 161-5 (2014)
PMID: 25043011

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-158233 (preferred)
Entry contents:
8 distinct polypeptide molecules
Macromolecules (8 distinct):
COP9 signalosome complex subunit 1 Chains: A, I
Molecule details ›
Chains: A, I
Length: 480 amino acids
Theoretical weight: 54.22 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13098 (Residues: 12-491; Coverage: 97%)
Gene names: COPS1, CSN1, GPS1
Sequence domains:
COP9 signalosome complex subunit 2 Chains: B, J
Molecule details ›
Chains: B, J
Length: 447 amino acids
Theoretical weight: 51.99 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P61201 (Residues: 1-443; Coverage: 100%)
Gene names: COPS2, CSN2, TRIP15
Sequence domains: PCI domain
COP9 signalosome complex subunit 3 Chains: C, K
Molecule details ›
Chains: C, K
Length: 423 amino acids
Theoretical weight: 47.92 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UNS2 (Residues: 1-423; Coverage: 100%)
Gene names: COPS3, CSN3
Sequence domains:
COP9 signalosome complex subunit 4 Chains: D, L
Molecule details ›
Chains: D, L
Length: 410 amino acids
Theoretical weight: 46.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BT78 (Residues: 1-406; Coverage: 100%)
Gene names: COPS4, CSN4
Sequence domains:
Structure domains: Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
COP9 signalosome complex subunit 5 Chains: E, M
Molecule details ›
Chains: E, M
Length: 334 amino acids
Theoretical weight: 37.62 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q92905 (Residues: 1-334; Coverage: 100%)
Gene names: COPS5, CSN5, JAB1
Sequence domains:
COP9 signalosome complex subunit 6 Chains: F, N
Molecule details ›
Chains: F, N
Length: 331 amino acids
Theoretical weight: 36.53 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q7L5N1 (Residues: 1-327; Coverage: 100%)
Gene names: COPS6, CSN6, HVIP
Sequence domains:
Structure domains: Cytidine Deaminase, domain 2
COP9 signalosome complex subunit 7a Chains: G, O
Molecule details ›
Chains: G, O
Length: 222 amino acids
Theoretical weight: 24.65 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9UBW8 (Residues: 1-218; Coverage: 79%)
Gene names: COPS7A, CSN7A, DERP10
Sequence domains:
COP9 signalosome complex subunit 8 Chains: H, P
Molecule details ›
Chains: H, P
Length: 212 amino acids
Theoretical weight: 23.44 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q99627 (Residues: 2-209; Coverage: 100%)
Gene names: COPS8, CSN8
Sequence domains: CSN8/PSMD8/EIF3K family

Ligands and Environments

1 bound ligand:
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P31
Unit cell:
a: 151.615Å b: 151.615Å c: 343.069Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.2 0.199 0.228
Expression system: Trichoplusia ni

Quick links

Citations

33 review citations

Protein neddylation: beyond cullin-RING ligases.
Enchev et al. (2015)
32 more

28 mentions without citation

Substrate specificity of the ubiquitin and Ubl proteases.
Ronau et al. (2016)
27 more