› 7zbz

Electron Microscopy
3.1Å resolution

CAND1 delhairpin-SCF-SKP2 CAND1 partly engaged SCF partly rocked

Released:
DOI: 10.2210/pdb7zbz/pdb
PDB entry 7zbz coloured by chain, front view.
PDB entry 7zbz coloured by chain, side view.
PDB entry 7zbz coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Systemwide disassembly and assembly of SCF ubiquitin ligase complexes.
Baek K, Scott DC, Henneberg LT, King MT, Mann M, Schulman BA
Cell (2023)
PMID: 37028429
Related structures: EMD-14597

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:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero pentamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-215426 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Cullin-1 Chain: C
Molecule details ›
Chain: C
Length: 776 amino acids
Theoretical weight: 89.8 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: Q13616 (Residues: 1-776; Coverage: 100%)
Gene name: CUL1
Sequence domains:
Cullin-associated NEDD8-dissociated protein 1 Chain: D
Molecule details ›
Chain: D
Length: 1238 amino acids
Theoretical weight: 137.31 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:
E3 ubiquitin-protein ligase RBX1 Chain: R
Molecule details ›
Chain: R
Length: 106 amino acids
Theoretical weight: 12.09 KDa
Source organism: Homo sapiens
Expression system: Trichoplusia ni
UniProt:
  • Canonical: P62877 (Residues: 5-108; Coverage: 96%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
S-phase kinase-associated protein 1 Chain: S
Molecule details ›
Chain: S
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: F
Molecule details ›
Chain: F
Length: 426 amino acids
Theoretical weight: 47.96 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

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-14597
Expression systems:
  • Trichoplusia ni
  • Escherichia coli BL21(DE3)

Quick links

Citations

3 citation in other articles

Activity-based profiling of cullin-RING E3 networks by conformation-specific probes.
Henneberg et al. (2023)
2 more

1 mention without citation

Systemwide disassembly and assembly of SCF ubiquitin ligase complexes.
Baek et al. (2023)