› 8or4

Electron Microscopy
3.8Å resolution

Partially dissociated CAND1-CUL1-RBX1-SKP1-SKP2-CKS1-CDK2

Released:
DOI: 10.2210/pdb8or4/pdb
PDB entry 8or4 coloured by chain, front view.
PDB entry 8or4 coloured by chain, side view.
PDB entry 8or4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural and mechanistic insights into the CAND1-mediated SCF substrate receptor exchange.
Shaaban M, Clapperton JA, Ding S, Kunzelmann S, Mäeots ME, Maslen SL, Skehel JM, Enchev RI
Mol Cell (2023)
PMID: 37339624
Related structures: EMD-17117

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
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero heptamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-219347 (preferred)
Entry contents:
7 distinct polypeptide molecules
Macromolecules (7 distinct):
Cullin-1 Chain: A
Molecule details ›
Chain: A
Length: 813 amino acids
Theoretical weight: 93.73 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q13616 (Residues: 1-776; Coverage: 100%)
Gene name: CUL1
Sequence domains:
E3 ubiquitin-protein ligase RBX1 Chain: B
Molecule details ›
Chain: B
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
Cullin-associated NEDD8-dissociated protein 1 Chain: C
Molecule details ›
Chain: C
Length: 1238 amino acids
Theoretical weight: 137.36 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q86VP6 (Residues: 1-1230; Coverage: 100%)
Gene names: CAND1, KIAA0829, TIP120, TIP120A
Sequence domains:
S-phase kinase-associated protein 1 Chain: D
Molecule details ›
Chain: D
Length: 163 amino acids
Theoretical weight: 18.68 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P63208 (Residues: 1-163; Coverage: 100%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
S-phase kinase-associated protein 2 Chain: E
Molecule details ›
Chain: E
Length: 429 amino acids
Theoretical weight: 48.34 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q13309 (Residues: 1-424; Coverage: 100%)
Gene names: FBXL1, SKP2
Sequence domains: F-box-like
Cyclin-dependent kinases regulatory subunit 1 Chain: G
Molecule details ›
Chain: G
Length: 74 amino acids
Theoretical weight: 8.89 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P61024 (Residues: 5-73; Coverage: 87%)
Gene names: CKS1, CKS1B, PNAS-143, PNAS-16
Sequence domains: Cyclin-dependent kinase regulatory subunit
Cyclin-dependent kinase 2 Chain: H
Molecule details ›
Chain: H
Length: 298 amino acids
Theoretical weight: 33.98 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P24941 (Residues: 1-298; Coverage: 100%)
Gene names: CDK2, CDKN2
Sequence domains: Protein kinase domain

Ligands and Environments

No bound ligands
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.8Å
Relevant EMDB volumes: EMD-17117
Expression systems:
  • Spodoptera frugiperda
  • Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

Dynamic molecular architecture and substrate recruitment of cullin3-RING E3 ligase CRL3KBTBD2.
Hu et al. (2024)
2 more

1 mention without citation

Protein neddylation and its role in health and diseases.
Zhang et al. (2024)