SAXSdb — 8ei1

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

Cullin-4B

Homo sapiens

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 × 8 PDB declaration: octameric（8） Consistent with protein copy count	Chain A； UniProt 206–557 Chain B； UniProt 206–557 Chain C； UniProt 206–557 Chain D； UniProt 206–557	Fragment：N-terminal domain	H316 × 4 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

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 8EI1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DO7 Solution structure of the winged helix-turn-helix motif of human CUL-4B Deposited 2006-04-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 808–895（88 aa） Fragment：winged helix-turn-helix motif	Not recorded	No recorded non-water small molecule	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
4A0C Structure of the CAND1-CUL4B-RBX1 complex Deposited 2011-09-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 mutation/modification Different oligomeric state Different ligand/ion 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 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

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 3–354； UniProt 206–557 Author chain B； PDBConstruct 3–354； UniProt 206–557 Author chain C； PDBConstruct 3–354； UniProt 206–557 Author chain D； PDBConstruct 3–354； UniProt 206–557

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8ei1
Deposition date deposition_date	2022-09-14
Structure title title	Crystal structure of the N-terminal domain of CUL4B in complex with H316, a Helicon Polypeptide
Keywords keywords	E3 ligase, complex, stapled peptide, LIGASE; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	40.05 Å
Radius of gyration Rg (electron density) rg_electron	39.48 Å
Forward intensity I(0) i0	419539000.00
Molecular weight molecular_weight	167830.0 kDa
Excluded volume excluded_volume	210680 Å³
Envelope volume envelope_volume	281360 Å³
Hydration-shell volume shell_volume	59592 Å³
Envelope diameter envelope_diameter	154.7 Å
Shell Rg shell_rg	44.80 Å
Envelope Rg envelope_rg	39.32 Å
Shape Rg shape_rg	39.51 Å
Total Rg total_rg	39.69 Å
Total atoms total_atoms	11809
Residues n_residues	1425
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	143.0 Å
Rg (real space) rg_real	40.06 Å
Rg uncertainty (real space) rg_real_error	1.31 Å
I(0) (real space) i0_real	4.1950e+08
I(0) uncertainty (real space) i0_real_error	7.8150e+06
Rg (reciprocal space) rg_reciprocal	40.05 Å
I(0) (reciprocal space) i0_reciprocal	419500000.0000
Solution quality estimate total_estimate	0.8550
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	47.7 Å
Skewness Skewness skewness	0.400
Kurtosis Kurtosis kurtosis	-0.087
Angular range angular_range	— – 0.1950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	39690000.0000
Real-space data points n_real_points	40
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.726; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.961

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Cullin-4B
Molecular weight formula_weight	41952.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	11809

SMPKLPENYTDETWQKLKEAVEAIQNSTSIKYNLEELYQAVENLCSYKISANLYKQLRQICEDHIKAQIHQFREDSLDSVLFLKKIDRCWQNHCRQMIMIRSIFLFLDRTYVLQNSMLPSIWDMGLELFRAHIISDQKVQNKTIDGILLLIERERNGEAIDRSLLRSLLSMLSDLQIYQDSFEQRFLEETNRLYAAEGQKLMQEREVPEYLHHVNKRLEEEADRLITYLDQTTQKSLIATVEKQLLGEHLTAILQKGLNNLLDENRIQDLSLLYQLFSRVRGGVQVLLQQWIEYIKAFGSTIVINPEKDKTMRQELDDFKDKVDHIIDICFLKNEKFINAMKEAFETFINKRPN

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	H316
Molecular weight formula_weight	2025.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

XDPADRWCELAAWTCDTFX

Entity 3 Entity 3 non-polymer

Description description	N,N'-(1,4-phenylene)diacetamide
Molecular weight formula_weight	192.2 kDa
Source method src_method	syn
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	99.650 Å
Unit-cell length b length_b	99.650 Å
Unit-cell length c length_c	366.490 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 43 21 2
Space-group number int_tables_number	96
Crystal system crystal_system	—

Resolution resolution	2.890 Å
Low-resolution limit resolution_low	49.820 Å
R factor r_factor	0.2137
R_work r_work	0.2116
R_free r_free	0.2544

fit	/app/data/saxs_computation/ei/8ei1/8ei1.fit
pddf	/app/data/pr_computation/ei/8ei1/8ei1.pr.out
profile	/app/data/saxs_computation/ei/8ei1/8ei1.dat

Crystal structure of the N-terminal domain of CUL4B in complex with H316, a Helicon Polypeptide

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

Cullin-4B

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)