SAXSdb — 3cbb

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

Hepatocyte Nuclear Factor 4-alpha, DNA binding domain

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–DNA Homooligomer Protein × 2 DNA 2 PDB declaration: tetrameric（4） Consistent with all polymer counts	Chain A； UniProt 58–135 Chain B； UniProt 58–135	Fragment：DNA binding domain	Hepatocyte Nuclear Factor 4-alpha promoter element DNA × 1 Hepatocyte Nuclear Factor 4-alpha promoter element DNA × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.8；298 K；26% PEG 4000, 80mM Magnesium acetate, 50mM Sodium citrate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.00 Å R-free 0.252

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 3CBB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1PZL Crystal structure of HNF4a LBD in complex with the ligand and the coactivator SRC-1 peptide Deposited 2003-07-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 133–369（237 aa） Fragment：HNF4A-LDB	Mutation：D137L, S138A	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；Sodium, Potassium Tartrate, Hepes, DTT, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K	Resolution 2.10 Å R-free 0.267
3FS1 Crystal structure of HNF4a LBD in complex with the ligand and the coactivator PGC-1a fragment Deposited 2009-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 148–377（230 aa） Fragment：HNF4a Ligand Binding Domain	Not recorded	MYR MYRISTIC ACID × 1	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å R-free 0.236
4B7W Ligand binding domain human hepatocyte nuclear factor 4alpha: Apo form Deposited 2012-08-24	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric	Chain A 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain B 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain C 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377 Chain D 142–377（236 aa） Fragment：LIGAND BINDING DOMAIN, RESIDUES 142-377	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；0.7 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, 10 MM DTT, 16% MPD IN 0.1 M TRIS, PH 8.0	Resolution 4.00 Å R-free 0.280
4IQR Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA Deposited 2013-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain A 55–377（323 aa） Fragment：unp residues 55-377 Chain B 55–377（323 aa） Fragment：unp residues 55-377	Not recorded	MYR MYRISTIC ACID × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.278
4IQR Multi-Domain Organization of the HNF4alpha Nuclear Receptor Complex on DNA Deposited 2013-01-13	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Heteromer；Protein × 4 PDB declaration: hexameric	Chain E 55–377（323 aa） Fragment：unp residues 55-377 Chain F 55–377（323 aa） Fragment：unp residues 55-377	Not recorded	MYR MYRISTIC ACID × 2 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；277 K；0.1M MES, 25mM NH4Cl, 25mM MgCl2 and PEG 3350 , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.90 Å R-free 0.278
6CHT HNF4alpha in complex with the corepressor EBP1 fragment Deposited 2018-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 178–421（244 aa） Chain B 178–421（244 aa） Chain J 178–421（244 aa） Chain K 178–421（244 aa） Chain M 178–421（244 aa） Chain N 178–421（244 aa） Chain V 178–421（244 aa） Chain W 178–421（244 aa）	Not recorded	DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274
6CHT HNF4alpha in complex with the corepressor EBP1 fragment Deposited 2018-02-22	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain D 178–421（244 aa） Chain E 178–421（244 aa） Chain G 178–421（244 aa） Chain H 178–421（244 aa） Chain P 178–421（244 aa） Chain Q 178–421（244 aa） Chain S 178–421（244 aa） Chain T 178–421（244 aa）	Not recorded	DAO LAURIC ACID × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.25；293 K；0.1 m Bis-Tris, 26-28% MPD, 3-4% PEG8000, 20-50 mM Glycine and 10% glycerol	Resolution 3.17 Å R-free 0.274
8C1L Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide Deposited 2022-12-20	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 148–377（230 aa） Chain B 148–377（230 aa）	Not recorded	PLM PALMITIC ACID × 2 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；284 K；20% PEG3350 -- 10% ethylene glycol -- 0.1M bis-tris-propane pH 8.5 -- 0.2M sodium nitrate	Resolution 2.00 Å R-free 0.237
9IBR Crystal structure of HNF4 alpha LBD complexed with GRIP-1 peptide and ESY13 Deposited 2025-02-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 148–377（230 aa）	Not recorded	A1I1W 2-hydroxy-5-(phenylethynyl)benzoic acid × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；289 K；16% PEG3350 8% ethylene glycol 0.1M bis-tris-propane pH 8.5 -	Resolution 2.78 Å R-free 0.355

7 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	HNF4A_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–78； UniProt 58–135 Author chain B； PDBConstruct 1–78； UniProt 58–135

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	3cbb
Deposition date deposition_date	2008-02-21
Structure title title	Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene Product
Keywords keywords	zinc finger, protein-DNA complex, diabetes, TRANSCRIPTION-DNA COMPLEX; TRANSCRIPTION/DNA
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	21.70 Å
Radius of gyration Rg (electron density) rg_electron	21.26 Å
Forward intensity I(0) i0	29505300.00
Molecular weight molecular_weight	30958.0 kDa
Excluded volume excluded_volume	34164 Å³
Envelope volume envelope_volume	46172 Å³
Hydration-shell volume shell_volume	18866 Å³
Envelope diameter envelope_diameter	75.0 Å
Shell Rg shell_rg	27.00 Å
Envelope Rg envelope_rg	21.59 Å
Shape Rg shape_rg	21.22 Å
Total Rg total_rg	21.95 Å
Total atoms total_atoms	2089
Residues n_residues	196
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	73.8 Å
Rg (real space) rg_real	21.78 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	2.9510e+07
I(0) uncertainty (real space) i0_real_error	3.7890e+05
Rg (reciprocal space) rg_reciprocal	21.77 Å
I(0) (reciprocal space) i0_reciprocal	29510000.0000
Solution quality estimate total_estimate	0.8703
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	22.0 Å
Skewness Skewness skewness	0.431
Kurtosis Kurtosis kurtosis	-0.328
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3888000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.823; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.853; Smooth: 0.989

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Hepatocyte Nuclear Factor 4-alpha promoter element DNA
Molecular weight formula_weight	6407.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C
Atom count atom_count	2246

TGAAGTCCAAAGTTCAGTCCC

Entity 2 Entity 2 polymer

Description description	Hepatocyte Nuclear Factor 4-alpha promoter element DNA
Molecular weight formula_weight	6478.2 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AGGGACTGAACTTTGGACTTC

Entity 3 Entity 3 polymer

Description description	Hepatocyte Nuclear Factor 4-alpha, DNA binding domain
Molecular weight formula_weight	9056.6 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B

ALCAICGDRATGKHYGASSCDGCKGFFRRSVRKNHMYSCRFSRQCVVDKDKRNQCRYCRLKKCFRAGMKKEAVQNERD

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 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	157

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3cbba_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

Domain ID domain_id	d3cbbb_
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.2 — Nuclear receptor

CATH v4.4 (2 domains)

Domain ID domain_id	3cbbA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

Domain ID domain_id	3cbbB00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily	10 — Erythroid Transcription Factor GATA-1, subunit A

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8. Citations (2)

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Unit-cell length a length_a	121.628 Å
Unit-cell length b length_b	35.425 Å
Unit-cell length c length_c	70.985 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	119.36 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	—
R_work r_work	0.2130
R_free r_free	0.2520

fit	/app/data/saxs_computation/cb/3cbb/3cbb.fit
pddf	/app/data/pr_computation/cb/3cbb/3cbb.pr.out
profile	/app/data/saxs_computation/cb/3cbb/3cbb.dat

Crystal Structure of Hepatocyte Nuclear Factor 4alpha in complex with DNA: Diabetes Gene Product

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

Hepatocyte Nuclear Factor 4-alpha, DNA binding domain

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)