8c1l

Crystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide

Method: X-RAY DIFFRACTION Dmax: 78.0 Å Quality: GOOD

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

Hepatocyte nuclear factor 4-alpha

Homo sapiens

UniProt P41235

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 148–377 Chain B; UniProt 148–377 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) 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

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.

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 1
Chains and sequence ranges Author chain A; PDBConstruct 3–232; UniProt 148–377 Author chain B; PDBConstruct 3–232; UniProt 148–377

Nuclear receptor coactivator 2

OrganismNot specified

UniProt Q15596

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain D; UniProt 687–695 Chain E; UniProt 687–695 Not recorded Hepatocyte nuclear factor 4-alpha × 2 (P41235) 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

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.

283 other PDB entries and 334 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NCOA2_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 1–9; UniProt 687–695 Author chain E; PDBConstruct 1–9; UniProt 687–695

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 8c1l

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 8c1l
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2. Structure Basics 2. Structure Basics

Entry ID entry_id8c1l
Deposition date deposition_date2022-12-20
最后修订 last_revision2024-01-10
Structure title titleCrystal structure of HNF4 alpha LBD in complexes with palmitic acid and GRIP-1 peptide
Keywords keywordscomplex, DNA BINDING PROTEIN; DNA BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.47
Radius of gyration Rg (electron density) rg_electron22.32
Forward intensity I(0) i038404900.00
Molecular weight molecular_weight50575.0 kDa
Excluded volume excluded_volume64565 ų
Envelope volume envelope_volume76541 ų
Hydration-shell volume shell_volume27778 ų
Envelope diameter envelope_diameter80.2
Shell Rg shell_rg29.83
Envelope Rg envelope_rg22.55
Shape Rg shape_rg22.31
Total Rg total_rg23.30
Total atoms total_atoms3557
Residues n_residues446
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 dmax78.0
Rg (real space) rg_real23.31
Rg uncertainty (real space) rg_real_error0.50
I(0) (real space) i0_real3.8400e+07
I(0) uncertainty (real space) i0_real_error5.8450e+05
Rg (reciprocal space) rg_reciprocal23.35
I(0) (reciprocal space) i0_reciprocal38410000.0000
Solution quality estimate total_estimate0.8766
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.2
Skewness Skewness skewness0.127
Kurtosis Kurtosis kurtosis-0.431
Angular range angular_range— – 0.3400 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha11180000.0000
Real-space data points n_real_points66
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.997

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)