3e00

Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with GW9662, 9-cis Retinoic Acid and NCOA2 Peptide

Method: X-RAY DIFFRACTION Dmax: 96.9 Å Quality: EXCELLENT

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

Retinoic acid receptor RXR-alpha

Homo sapiens

UniProt P19793

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain A; UniProt 11–462 Fragment:UNP residues 11-462 Peroxisome proliferator-activated receptor gamma × 1 (P37231) ;DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3') ; × 1 NCOA2 Peptide × 2 (Q15596) ZN ZINC ION × 4 9CR (9cis)-retinoic acid × 1 GW9 2-chloro-5-nitro-N-phenylbenzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;15-18% PEG 3350, 25mM MgCl2, 100mM NH4Cl, 5mM DTT and 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.10 Å R-free 0.276

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.

107 other PDB entries and 138 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RXRA_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 16–467; UniProt 11–462

Peroxisome proliferator-activated receptor gamma

Homo sapiens

UniProt P37231

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 Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain D; UniProt 102–505 Fragment:UNP residues 102-505 Retinoic acid receptor RXR-alpha × 1 (P19793) ;DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3') ; × 1 NCOA2 Peptide × 2 (Q15596) ZN ZINC ION × 4 9CR (9cis)-retinoic acid × 1 GW9 2-chloro-5-nitro-N-phenylbenzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;15-18% PEG 3350, 25mM MgCl2, 100mM NH4Cl, 5mM DTT and 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.10 Å R-free 0.276

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.

369 other PDB entries and 500 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PPARG_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain D; PDBConstruct 16–419; UniProt 102–505

NCOA2 Peptide

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–DNA Heteromer Protein × 4 DNA 2 PDB declaration: hexameric(6) Consistent with all polymer counts Chain E; UniProt 685–697 Chain G; UniProt 685–697 Not recorded Retinoic acid receptor RXR-alpha × 1 (P19793) Peroxisome proliferator-activated receptor gamma × 1 (P37231) ;DNA (5'-D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DTP*DCP*DAP*DG)-3') ; × 1 ;DNA (5'-D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DTP*DTP*DTP*DG)-3') ; × 1 ZN ZINC ION × 4 9CR (9cis)-retinoic acid × 1 GW9 2-chloro-5-nitro-N-phenylbenzamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 6.5;277 K;15-18% PEG 3350, 25mM MgCl2, 100mM NH4Cl, 5mM DTT and 0.1M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K Resolution 3.10 Å R-free 0.276

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 5
Chains and sequence ranges Author chain E; PDBConstruct 1–13; UniProt 685–697 Author chain G; PDBConstruct 1–13; UniProt 685–697

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 3e00

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3e00
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id3e00
Deposition date deposition_date2008-07-30
Structure title titleIntact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with GW9662, 9-cis Retinoic Acid and NCOA2 Peptide
Keywords keywords;DNA-binding, Host-virus interaction, Metal-binding, Nucleus, Receptor, Transcription, Transcription regulation, Zinc-finger, Activator, Diabetes mellitus, Disease mutation, Obesity, Phosphoprotein, Transcription-DNA COMPLEX ;; Transcription/DNA
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier31.11
Radius of gyration Rg (electron density) rg_electron29.73
Forward intensity I(0) i0150231000.00
Molecular weight molecular_weight89981.0 kDa
Excluded volume excluded_volume109670 ų
Envelope volume envelope_volume142190 ų
Hydration-shell volume shell_volume39731 ų
Envelope diameter envelope_diameter103.8
Shell Rg shell_rg37.08
Envelope Rg envelope_rg29.30
Shape Rg shape_rg29.69
Total Rg total_rg30.50
Total atoms total_atoms6244
Residues n_residues711
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 dmax96.9
Rg (real space) rg_real31.00
Rg uncertainty (real space) rg_real_error0.53
I(0) (real space) i0_real1.5020e+08
I(0) uncertainty (real space) i0_real_error2.0360e+06
Rg (reciprocal space) rg_reciprocal31.05
I(0) (reciprocal space) i0_reciprocal150200000.0000
Solution quality estimate total_estimate0.9037
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary39.9
Skewness Skewness skewness0.194
Kurtosis Kurtosis kurtosis-0.458
Angular range angular_range— – 0.2550 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha15580000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.950; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.893

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (8)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id3e00A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id3e00A02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3e00D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology50 — Erythroid Transcription Factor GATA-1; Chain A
Homologous superfamily homologous superfamily10 — Erythroid Transcription Factor GATA-1, subunit A
Domain ID domain_id3e00D02
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)