› 8h3a

Electron Microscopy
7.51Å resolution

Cryo-EM Structure of the KBTBD2-CRL3~N8(removed)-CSN complex

Released:
DOI: 10.2210/pdb8h3a/pdb
PDB entry 8h3a coloured by chain, front view.
PDB entry 8h3a coloured by chain, side view.
PDB entry 8h3a coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3KBTBD2.
Hu Y, Zhang Z, Mao Q, Zhang X, Hao A, Xun Y, Wang Y, Han L, Zhan W, Liu Q, Yin Y, Peng C, Moresco EMY, Chen Z, Beutler B, Sun L
Nat Struct Mol Biol 31 336-350 (2024)
PMID: 38332366
Related structures: EMD-34462

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:

Structure analysis Details

Assembly composition:
hetero dodecamer (preferred)
PDBe Complex ID:
PDB-CPX-231827 (preferred)
Entry contents:
11 distinct polypeptide molecules
Macromolecules (11 distinct):
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: Trichoplusia ni
UniProt:
  • Canonical: Q92905 (Residues: 1-334; Coverage: 100%)
Gene names: COPS5, CSN5, JAB1
Sequence domains:
COP9 signalosome complex subunit 1 Chain: A
Molecule details ›
Chain: A
Length: 527 amino acids
Theoretical weight: 59.12 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 Chain: B
Molecule details ›
Chain: B
Length: 443 amino acids
Theoretical weight: 51.66 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 Chain: C
Molecule details ›
Chain: C
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 Chain: D
Molecule details ›
Chain: D
Length: 406 amino acids
Theoretical weight: 46.32 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9BT78 (Residues: 1-406; Coverage: 100%)
Gene names: COPS4, CSN4
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: Trichoplusia ni
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: 264 amino acids
Theoretical weight: 29.66 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q9H9Q2 (Residues: 1-264; Coverage: 100%)
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: Trichoplusia ni
UniProt:
  • Canonical: Q99627 (Residues: 1-209; Coverage: 100%)
Gene names: COPS8, CSN8
Sequence domains: CSN8/PSMD8/EIF3K family
Kelch repeat and BTB domain-containing protein 2 Chains: I, M
Molecule details ›
Chains: I, M
Length: 623 amino acids
Theoretical weight: 71.43 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8IY47 (Residues: 1-623; Coverage: 100%)
Gene names: BKLHD1, CGI-73, KBTBD2, KIAA1489
Sequence domains:
Cullin-3 Chain: L
Molecule details ›
Chain: L
Length: 768 amino acids
Theoretical weight: 89.06 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13618 (Residues: 1-768; Coverage: 100%)
Gene names: CUL3, KIAA0617
Sequence domains:
E3 ubiquitin-protein ligase RBX1 Chain: R
Molecule details ›
Chain: R
Length: 108 amino acids
Theoretical weight: 12.29 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain

Ligands and Environments

1 bound ligand:
Ligand ZN 4 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 7.51Å
Relevant EMDB volumes: EMD-34462
Expression systems:
  • Trichoplusia ni
  • Spodoptera frugiperda

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