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2do7

Solution structure of the winged helix-turn-helix motif of human CUL-4B

Method: SOLUTION NMR Dmax: 48.0 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 808–895 Fragment：winged helix-turn-helix motif No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：0.8mM 13C/15N-PROTEIN, 20mM d-Tris-HCl(pH7.0), 100mM NaCl, 1mM d-DTT, 0.02% NaN3, 10% D2O | 90% H2O/10% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 2DO7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4A0C Structure of the CAND1-CUL4B-RBX1 complex Deposited 2011-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain E 192–913（722 aa）
Not recorded 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
4A0C Structure of the CAND1-CUL4B-RBX1 complex Deposited 2011-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 192–913（722 aa）
Not recorded 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
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain E 192–913（722 aa） Fragment：RESIDUES 193-913
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A0L Structure of DDB1-DDB2-CUL4B-RBX1 bound to a 12 bp abasic site containing DNA-duplex Deposited 2011-09-09 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric
Chain H 192–913（722 aa） Fragment：RESIDUES 193-913
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 6.2；100MM MES PH 6.2, 3.1% PEG 6000, 4% ETHYLENEGLYCOL
Resolution 7.40 Å R-free 0.320
4A64 Crystal structure of the N-terminal domain of human Cul4B at 2.57A resolution Deposited 2011-10-31 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 188–539（352 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 188-539
Chain B 188–539（352 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 188-539
Chain C 188–539（352 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 188-539
Chain D 188–539（352 aa） Fragment：N-TERMINAL DOMAIN, RESIDUES 188-539
Mutation：YES Mutation：YES Mutation：YES Mutation：YES EDO 1,2-ETHANEDIOL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions 24% PEG4000, 100 MM LISO4, 100 MM TRIS (PH 8.2)
Resolution 2.57 Å R-free 0.230
8EI1 Crystal structure of the N-terminal domain of CUL4B in complex with H316, a Helicon Polypeptide Deposited 2022-09-14 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric
Chain A 206–557（352 aa） Fragment：N-terminal domain
Chain B 206–557（352 aa） Fragment：N-terminal domain
Chain C 206–557（352 aa） Fragment：N-terminal domain
Chain D 206–557（352 aa） Fragment：N-terminal domain
Not recorded WHL N,N'-(1,4-phenylene)diacetamide × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；291 K；0.2 M Lithium sulfate, 0.1 M Tris pH 8.5, 30% w/v PEG 4000
Resolution 2.89 Å R-free 0.254

4 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CUL4B_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–95； UniProt 808–895

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 2do7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2do7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2do7
Deposition date deposition_date2006-04-27
Structure title titleSolution structure of the winged helix-turn-helix motif of human CUL-4B
Keywords keywords;helix-turn-helix motif, structural genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, PROTEIN BINDING ;; PROTEIN BINDING
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier17.80 Å
Radius of gyration Rg (electron density) rg_electron16.95 Å
Forward intensity I(0) i0816967000.00
Molecular weight molecular_weight230820.0 kDa
Excluded volume excluded_volume285840 ų
Envelope volume envelope_volume89093 ų
Hydration-shell volume shell_volume29308 ų
Envelope diameter envelope_diameter99.7 Å
Shell Rg shell_rg32.50 Å
Envelope Rg envelope_rg26.22 Å
Shape Rg shape_rg16.91 Å
Total Rg total_rg17.66 Å
Total atoms total_atoms32320
Residues n_residues2020
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax48.0 Å
Rg (real space) rg_real16.77 Å
Rg uncertainty (real space) rg_real_error0.08 Å
I(0) (real space) i0_real7.7820e+08
I(0) uncertainty (real space) i0_real_error7.1040e+06
Rg (reciprocal space) rg_reciprocal18.04 Å
I(0) (reciprocal space) i0_reciprocal817000000.0000
Solution quality estimate total_estimate0.6798
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary17.5 Å
Skewness Skewness skewness0.394
Kurtosis Kurtosis kurtosis-0.480
Angular range angular_range— – 0.4450 Å−1
Current regularization parameter α current_alpha4.5040
Highest regularization parameter α highest_alpha429700.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.004; Oscil: 0.968; Stabil: 0.985; Sysdev: 0.000; Positv: 1.000; Valcen: 0.979; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2do7A01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily10 — Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain
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8. Citations (1)

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9. Files and Curves (10)