1zdu

The Crystal Structure of Human Liver Receptor Homologue-1

Method: X-RAY DIFFRACTION Dmax: 62.8 Å Quality: GOOD

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

Orphan nuclear receptor NR5A2

Homo sapiens

UniProt O00482

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 297–541 Not recorded Nuclear receptor coactivator 2 × 2 (Q15596) P3A PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;NaH2PO4, K2HPO4, pH 7.5, temperature 293K, VAPOR DIFFUSION, SITTING DROP Resolution 2.50 Å R-free 0.281

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.

26 other PDB entries and 38 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NR5A2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–245; UniProt 297–541

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain P; UniProt 741–751 Chain Q; UniProt 741–751 Fragment:residues 741-751 Orphan nuclear receptor NR5A2 × 1 (O00482) P3A PHOSPHATIDYLGLYCEROL-PHOSPHOGLYCEROL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293 K;NaH2PO4, K2HPO4, pH 7.5, temperature 293K, VAPOR DIFFUSION, SITTING DROP Resolution 2.50 Å R-free 0.281

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 P; PDBConstruct 1–11; UniProt 741–751 Author chain Q; PDBConstruct 1–11; UniProt 741–751

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 1zdu

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1zdu
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1zdu
Deposition date deposition_date2005-04-14
Structure title titleThe Crystal Structure of Human Liver Receptor Homologue-1
Keywords keywordsLiver Receptor Homologue-1, LRH-1, Nuclear Receptor, phospholipid, phosphatidylethanolamine, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier19.94
Radius of gyration Rg (electron density) rg_electron18.44
Forward intensity I(0) i014923700.00
Molecular weight molecular_weight30423.0 kDa
Excluded volume excluded_volume38719 ų
Envelope volume envelope_volume44557 ų
Hydration-shell volume shell_volume19935 ų
Envelope diameter envelope_diameter65.8
Shell Rg shell_rg25.04
Envelope Rg envelope_rg18.77
Shape Rg shape_rg18.44
Total Rg total_rg19.47
Total atoms total_atoms2135
Residues n_residues254
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 dmax62.8
Rg (real space) rg_real19.81
Rg uncertainty (real space) rg_real_error0.30
I(0) (real space) i0_real1.4920e+07
I(0) uncertainty (real space) i0_real_error1.6750e+05
Rg (reciprocal space) rg_reciprocal19.83
I(0) (reciprocal space) i0_reciprocal14920000.0000
Solution quality estimate total_estimate0.8950
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary25.6
Skewness Skewness skewness0.158
Kurtosis Kurtosis kurtosis-0.406
Angular range angular_range— – 0.4000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha2875000.0000
Real-space data points n_real_points72
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.886; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.978

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1zdua_
Class classa — All alpha proteins
Fold Fold folda.123 — Nuclear receptor ligand-binding domain
Superfamily Superfamily superfamilya.123.1 — Nuclear receptor ligand-binding domain
Family Family familya.123.1.1 — Nuclear receptor ligand-binding domain

CATH v4.4 (1 domains)

Domain ID domain_id1zduA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor

8. Citations (1)

9. Files and Curves (10)