1zdt

The Crystal Structure of Human Steroidogenic Factor-1

Method: X-RAY DIFFRACTION Dmax: 93.7 Å Quality: GOOD

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

Steroidogenic factor 1

Homo sapiens

UniProt Q13285

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 221–461 Mutation:C247S, C412S Nuclear receptor coactivator 2 × 1 (Q15596) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 221–461 Mutation:C247S, C412S Nuclear receptor coactivator 2 × 1 (Q15596) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 221–461 Chain B; UniProt 221–461 Mutation:C247S, C412S Nuclear receptor coactivator 2 × 2 (Q15596) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265

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.

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

View Construct and Data Evidence
UniProt name STF1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–241; UniProt 221–461 Author chain B; PDBConstruct 1–241; UniProt 221–461

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain P; UniProt 741–752 Fragment:residues 741-752 Steroidogenic factor 1 × 1 (Q13285) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain Q; UniProt 741–752 Fragment:residues 741-752 Steroidogenic factor 1 × 1 (Q13285) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265
3 Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain P; UniProt 741–752 Chain Q; UniProt 741–752 Fragment:residues 741-752 Steroidogenic factor 1 × 2 (Q13285) PEF DI-PALMITOYL-3-SN-PHOSPHATIDYLETHANOLAMINE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;277 K;PEG3350, ammonium sulfate, sucrose, pH 5.5, temperature 277K, VAPOR DIFFUSION, SITTING DROP Resolution 2.10 Å R-free 0.265

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 332 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 1–12; UniProt 741–752 Author chain Q; PDBConstruct 1–12; UniProt 741–752

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 1zdt

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1zdt
Deposition date deposition_date2005-04-14
Structure title titleThe Crystal Structure of Human Steroidogenic Factor-1
Keywords keywordsSteroidogenic Factor-1, Nuclear Receptor, pholpholipid, phosphatidylethanolamine, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.41
Radius of gyration Rg (electron density) rg_electron29.69
Forward intensity I(0) i050095000.00
Molecular weight molecular_weight58183.0 kDa
Excluded volume excluded_volume74152 ų
Envelope volume envelope_volume97137 ų
Hydration-shell volume shell_volume27353 ų
Envelope diameter envelope_diameter94.1
Shell Rg shell_rg36.89
Envelope Rg envelope_rg28.95
Shape Rg shape_rg29.70
Total Rg total_rg30.42
Total atoms total_atoms4085
Residues n_residues495
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 dmax93.7
Rg (real space) rg_real30.43
Rg uncertainty (real space) rg_real_error0.63
I(0) (real space) i0_real5.0100e+07
I(0) uncertainty (real space) i0_real_error7.0760e+05
Rg (reciprocal space) rg_reciprocal30.43
I(0) (reciprocal space) i0_reciprocal50090000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary27.0
Skewness Skewness skewness0.212
Kurtosis Kurtosis kurtosis-0.836
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha13720000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.911; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.941; Smooth: 0.865

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id1zdtA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id1zdtB00
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)