› 1ldk

X-ray diffraction
3.1Å resolution

Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF Ubiquitin Ligase Complex

Released:
DOI: 10.2210/pdb1ldk/pdb
PDB entry 1ldk coloured by chain, front view.
PDB entry 1ldk coloured by chain, side view.
PDB entry 1ldk coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure of the Cul1-Rbx1-Skp1-F boxSkp2 SCF ubiquitin ligase complex.
Zheng N, Schulman BA, Song L, Miller JJ, Jeffrey PD, Wang P, Chu C, Koepp DM, Elledge SJ, Pagano M, Conaway RC, Conaway JW, Harper JW, Pavletich NP
Nature 416 703-9 (2002)
PMID: 11961546

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 domains:

Structure analysis Details

Assemblies composition:
hetero pentamer (preferred)
hetero decamer
Assembly name:
PDBe Complex ID:
PDB-CPX-158744 (preferred)
Entry contents:
5 distinct polypeptide molecules
Macromolecules (5 distinct):
Cullin-1 Chain: A
Molecule details ›
Chain: A
Length: 396 amino acids
Theoretical weight: 45.75 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13616 (Residues: 15-410; Coverage: 51%)
Gene name: CUL1
Sequence domains: Cullin family
Structure domains: Cullin Repeats
Cullin-1 Chain: B
Molecule details ›
Chain: B
Length: 366 amino acids
Theoretical weight: 42.51 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13616 (Residues: 411-776; Coverage: 47%)
Gene name: CUL1
Sequence domains:
Structure domains:
E3 ubiquitin-protein ligase RBX1, N-terminally processed Chain: C
Molecule details ›
Chain: C
Length: 90 amino acids
Theoretical weight: 10.66 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P62877 (Residues: 19-108; Coverage: 83%)
Gene names: RBX1, RNF75, ROC1
Sequence domains: RING-H2 zinc finger domain
Structure domains: Zinc/RING finger domain, C3HC4 (zinc finger)
S-phase kinase-associated protein 1 Chain: D
Molecule details ›
Chain: D
Length: 133 amino acids
Theoretical weight: 15.03 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P63208 (Residues: 2-140; Coverage: 82%)
Gene names: EMC19, OCP2, SKP1, SKP1A, TCEB1L
Sequence domains:
Structure domains: Potassium Channel Kv1.1; Chain A
S-phase kinase-associated protein 2 Chain: E
Molecule details ›
Chain: E
Length: 41 amino acids
Theoretical weight: 4.76 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q13309 (Residues: 97-137; Coverage: 10%)
Gene names: FBXL1, SKP2
Sequence domains: F-box-like
Structure domains: Monooxygenase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: CHESS BEAMLINE A1
Spacegroup: P21212
Unit cell:
a: 219.378Å b: 50.529Å c: 158.61Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.289 0.289 0.331
Expression system: Escherichia coli

Quick links

Citations

220 review citations

RING domain E3 ubiquitin ligases.
Deshaies et al. (2009)
219 more

67 mentions without citation

Mechanism of CRL4(Cdt2), a PCNA-dependent E3 ubiquitin ligase.
Havens et al. (2011)
66 more