4a0c

Structure of the CAND1-CUL4B-RBX1 complex

Method: X-RAY DIFFRACTION Dmax: 198.0 Å Quality: REASONABLE

1. Protein Identity and Related Structures Protein Identity & Related Structures

CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1

HOMO SAPIENS

UniProt Q86VP6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–1230 Not recorded CULLIN-4B × 1 (Q13620) E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 (P62878) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 1–1230 Not recorded CULLIN-4B × 1 (Q13620) E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 (P62878) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

13 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CAND1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 24–1253; UniProt 1–1230 Author chain B; PDBConstruct 24–1253; UniProt 1–1230

CULLIN-4B

HOMO SAPIENS

UniProt Q13620

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain E; UniProt 192–913 Not recorded CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1 × 1 (Q86VP6) E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 (P62878) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 192–913 Not recorded CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1 × 1 (Q86VP6) E3 UBIQUITIN-PROTEIN LIGASE RBX1 × 1 (P62878) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL4B_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 20–741; UniProt 192–913 Author chain E; PDBConstruct 20–741; UniProt 192–913

E3 UBIQUITIN-PROTEIN LIGASE RBX1

MUS MUSCULUS

UniProt P62878

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 12–108 Not recorded CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1 × 1 (Q86VP6) CULLIN-4B × 1 (Q13620) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 12–108 Not recorded CULLIN-ASSOCIATED NEDD8-DISSOCIATED PROTEIN 1 × 1 (Q86VP6) CULLIN-4B × 1 (Q13620) ZN ZINC ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions:pH 6.3;100 MM MES PH 6.3, 30% PEG 200, 2% PEG 8000. Resolution 3.80 Å R-free 0.319

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

4 other PDB entries and 5 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RBX1_MOUSE
Isoform
PDB entities 3
Chains and sequence ranges Author chain D; PDBConstruct 2–98; UniProt 12–108 Author chain F; PDBConstruct 2–98; UniProt 12–108

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 4a0c

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4a0c
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4a0c
Deposition date deposition_date2011-09-08
Structure title titleStructure of the CAND1-CUL4B-RBX1 complex
Keywords keywordsTRANSCRIPTION, LIGASE, UBIQUITIN, CELL CYCLE, DNA DAMAGE REPAIR; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier65.47
Radius of gyration Rg (electron density) rg_electron65.88
Forward intensity I(0) i02580550000.00
Molecular weight molecular_weight439450.0 kDa
Excluded volume excluded_volume555470 ų
Envelope volume envelope_volume901760 ų
Hydration-shell volume shell_volume116060 ų
Envelope diameter envelope_diameter222.4
Shell Rg shell_rg65.36
Envelope Rg envelope_rg64.16
Shape Rg shape_rg65.91
Total Rg total_rg65.75
Total atoms total_atoms30804
Residues n_residues3866
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax198.0
Rg (real space) rg_real65.80
Rg uncertainty (real space) rg_real_error1.35
I(0) (real space) i0_real2.5800e+09
I(0) uncertainty (real space) i0_real_error4.5320e+07
Rg (reciprocal space) rg_reciprocal65.10
I(0) (reciprocal space) i0_reciprocal2577000000.0000
Solution quality estimate total_estimate0.6139
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary66.0
Skewness Skewness skewness0.398
Kurtosis Kurtosis kurtosis-0.494
Angular range angular_range— – 0.1200 −1
Current regularization parameter α current_alpha0.0002
Highest regularization parameter α highest_alpha200600000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.978; Stabil: 1.000; Sysdev: 0.013; Positv: 1.000; Valcen: 0.999; Smooth: 0.005

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id4a0cA00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4a0cB00
Class class1 — Mainly Alpha
Architecture architecture25 — Alpha Horseshoe
Topology topology10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily10 — Leucine-rich Repeat Variant
Domain ID domain_id4a0cD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)
Domain ID domain_id4a0cF00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology40 — Herpes Virus-1
Homologous superfamily homologous superfamily10 — Zinc/RING finger domain, C3HC4 (zinc finger)

8. Citations (1)

9. Files and Curves (10)