› 8b3i

Electron Microscopy
3.5Å resolution

CRL4CSA-E2-Ub (state 2)

Released:
DOI: 10.2210/pdb8b3i/pdb
PDB entry 8b3i coloured by chain, front view.
PDB entry 8b3i coloured by chain, side view.
PDB entry 8b3i coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Kokic G, Cramer P
Related structures: EMD-15829

Function and Biology Details

Reactions catalysed: 
S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine
(1a) S-ubiquitinyl-[E1 ubiquitin-activating enzyme]-L-cysteine + [(E3-independent) E2 ubiquitin-conjugating enzyme]-L-cysteine = [E1 ubiquitin-activating enzyme]-L-cysteine + S-monoubiquitinyl-[(E3-independent) ubiquitin-conjugating enzyme]-L-cysteine
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 heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-229876 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Ubiquitin-conjugating enzyme E2 D2 Chain: D
Molecule details ›
Chain: D
Length: 147 amino acids
Theoretical weight: 16.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62837 (Residues: 1-147; Coverage: 100%)
Gene names: PUBC1, UBC4, UBC5B, UBCH4, UBCH5B, UBE2D2
Sequence domains: Ubiquitin-conjugating enzyme
NEDD8 Chain: N
Molecule details ›
Chain: N
Length: 76 amino acids
Theoretical weight: 8.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q15843 (Residues: 1-76; Coverage: 94%)
Gene name: NEDD8
Sequence domains: Ubiquitin family
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: Trichoplusia ni
UniProt:
  • Canonical: P62877 (Residues: 1-108; Coverage: 100%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Ubiquitin Chain: U
Molecule details ›
Chain: U
Length: 76 amino acids
Theoretical weight: 8.58 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P0CG48 (Residues: 609-684; Coverage: 11%)
Gene name: UBC
Sequence domains: Ubiquitin family
DNA excision repair protein ERCC-8 Chain: a
Molecule details ›
Chain: a
Length: 396 amino acids
Theoretical weight: 44.11 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13216 (Residues: 1-396; Coverage: 100%)
Gene names: CKN1, CSA, ERCC8
Sequence domains: WD domain, G-beta repeat
DNA damage-binding protein 1 Chain: d
Molecule details ›
Chain: d
Length: 1140 amino acids
Theoretical weight: 127.1 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q16531 (Residues: 1-1140; Coverage: 100%)
Gene names: DDB1, XAP1
Sequence domains:
Cullin-4A Chain: e
Molecule details ›
Chain: e
Length: 759 amino acids
Theoretical weight: 87.81 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13619 (Residues: 1-759; Coverage: 100%)
Gene name: CUL4A
Sequence domains:

Ligands and Environments

1 bound ligand:
Ligand ZN 3 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.5Å
Relevant EMDB volumes: EMD-15829
Expression systems:
  • Escherichia coli
  • Trichoplusia ni

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