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

X-ray diffraction
3.1Å resolution
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
Assemblies composition:
hetero pentamer (preferred)
hetero decamer
Entry contents: 5 distinct polypeptide molecules

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Assemblies

Assembly 1 (preferred)
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Assembly Name: SCF E3 ubiquitin ligase complex, SKP2 variant
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Multimeric state: hetero pentamer
Accessible surface area: 51511.11 Å2
Buried surface area: 9967.28 Å2
Dissociation area: 938.19 Å2
Dissociation energy (ΔGdiss): 2.2 kcal/mol
Dissociation entropy (TΔSdiss): 14.33 kcal/mol
Symmetry number: 1
PDBe Complex ID: PDB-CPX-158744
Assembly 2
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Multimeric state: hetero decamer
Accessible surface area: 99810.9 Å2
Buried surface area: 23157.85 Å2
Dissociation area: 1,609.78 Å2
Dissociation energy (ΔGdiss): 5.64 kcal/mol
Dissociation entropy (TΔSdiss): 17.13 kcal/mol
Symmetry number: 2
PDBe Complex ID: PDB-CPX-158752

Macromolecules

Cullin-1
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
Pfam: Cullin family
InterPro:
CATH: Cullin Repeats
SCOP: Cullin repeat
Cullin-1 in PDB entry 1ldk, assembly 1, front view.
Cullin-1 in PDB entry 1ldk, assembly 1, side view.
Cullin-1 in PDB entry 1ldk, assembly 1, top view.
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Cullin-1
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
Pfam:
InterPro:
CATH:
SCOP:
Cullin-1 in PDB entry 1ldk, assembly 1, front view.
Cullin-1 in PDB entry 1ldk, assembly 1, side view.
Cullin-1 in PDB entry 1ldk, assembly 1, top view.
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E3 ubiquitin-protein ligase RBX1, N-terminally processed
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
Pfam: RING-H2 zinc finger domain
InterPro:
CATH: Zinc/RING finger domain, C3HC4 (zinc finger)
SCOP: RING finger domain, C3HC4
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 1ldk, assembly 1, front view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 1ldk, assembly 1, side view.
E3 ubiquitin-protein ligase RBX1, N-terminally processed in PDB entry 1ldk, assembly 1, top view.
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S-phase kinase-associated protein 1
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
Pfam:
InterPro:
CATH: Potassium Channel Kv1.1; Chain A
SCOP:
S-phase kinase-associated protein 1 in PDB entry 1ldk, assembly 1, front view.
S-phase kinase-associated protein 1 in PDB entry 1ldk, assembly 1, side view.
S-phase kinase-associated protein 1 in PDB entry 1ldk, assembly 1, top view.
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S-phase kinase-associated protein 2
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
Pfam: F-box-like
InterPro:
CATH: Monooxygenase
SCOP: F-box domain
S-phase kinase-associated protein 2 in PDB entry 1ldk, assembly 1, front view.
S-phase kinase-associated protein 2 in PDB entry 1ldk, assembly 1, side view.
S-phase kinase-associated protein 2 in PDB entry 1ldk, assembly 1, top view.
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