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

Electron Microscopy
5.9Å resolution
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
Assembly composition:
hetero tridecamer (preferred)
Entry contents: 13 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Multimeric state: hetero tridecamer
PDBe Complex ID: PDB-CPX-158230

Macromolecules

COP9 signalosome complex subunit 1
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
Pfam:
InterPro:
COP9 signalosome complex subunit 1 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 1 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 1 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 2
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
Pfam: PCI domain
InterPro:
COP9 signalosome complex subunit 2 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 2 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 2 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 3
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
Pfam:
InterPro:
COP9 signalosome complex subunit 3 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 3 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 3 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 4
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
Pfam:
InterPro:
COP9 signalosome complex subunit 4 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 4 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 4 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 5
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
Pfam:
InterPro:
COP9 signalosome complex subunit 5 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 5 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 5 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 6
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
Pfam:
InterPro:
COP9 signalosome complex subunit 6 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 6 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 6 in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 7b
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%)
  • Best match: Q9H9Q2-3 (Residues: 1-212)
Gene names: COPS7B, CSN7B
Pfam:
InterPro:
COP9 signalosome complex subunit 7b in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 7b in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 7b in PDB entry 6r7i, assembly 1, top view.
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COP9 signalosome complex subunit 8
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
Pfam: CSN8/PSMD8/EIF3K family
InterPro:
COP9 signalosome complex subunit 8 in PDB entry 6r7i, assembly 1, front view.
COP9 signalosome complex subunit 8 in PDB entry 6r7i, assembly 1, side view.
COP9 signalosome complex subunit 8 in PDB entry 6r7i, assembly 1, top view.
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NEDD8
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
Pfam: Ubiquitin family
InterPro:
NEDD8 in PDB entry 6r7i, assembly 1, front view.
NEDD8 in PDB entry 6r7i, assembly 1, side view.
NEDD8 in PDB entry 6r7i, assembly 1, top view.
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Cullin-2
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
Pfam:
InterPro:
Cullin-2 in PDB entry 6r7i, assembly 1, front view.
Cullin-2 in PDB entry 6r7i, assembly 1, side view.
Cullin-2 in PDB entry 6r7i, assembly 1, top view.
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Elongin-B
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
Pfam: Ubiquitin family
InterPro:
Elongin-B in PDB entry 6r7i, assembly 1, front view.
Elongin-B in PDB entry 6r7i, assembly 1, side view.
Elongin-B in PDB entry 6r7i, assembly 1, top view.
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Elongin-C
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
Pfam: Skp1 family, tetramerisation domain
InterPro:
Elongin-C in PDB entry 6r7i, assembly 1, front view.
Elongin-C in PDB entry 6r7i, assembly 1, side view.
Elongin-C in PDB entry 6r7i, assembly 1, top view.
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E3 ubiquitin-protein ligase RBX1, N-terminally processed
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
Pfam: RING-H2 zinc finger domain
InterPro:
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 6r7i, assembly 1, front view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 6r7i, assembly 1, side view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 6r7i, assembly 1, top view.
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