2gpp

Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716

Method: X-RAY DIFFRACTION Dmax: 73.6 Å Quality: EXCELLENT

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

Estrogen-related receptor gamma

Homo sapiens

UniProt P62508

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 229–458 Chain B; UniProt 229–458 Fragment:Residues (229-458) Nuclear receptor-interacting protein 1 × 2 (P48552) 1BA 4-HYDROXY-N'-(4-ISOPROPYLBENZYL)BENZOHYDRAZIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K Resolution 2.60 Å R-free 0.257

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.

35 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ERR3_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–230; UniProt 229–458 Author chain B; PDBConstruct 1–230; UniProt 229–458

Nuclear receptor-interacting protein 1

OrganismNot specified

UniProt P48552

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 C; UniProt 366–390 Chain D; UniProt 366–390 Fragment:Residues (366-390) Estrogen-related receptor gamma × 2 (P62508) 1BA 4-HYDROXY-N'-(4-ISOPROPYLBENZYL)BENZOHYDRAZIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;295 K;9% PEG 20K 0.1M MES buffer, pH 7.5, vapor diffusion, hanging drop, temperature 295K Resolution 2.60 Å R-free 0.257

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.

15 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NRIP1_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 1–25; UniProt 366–390 Author chain D; PDBConstruct 1–25; UniProt 366–390

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 2gpp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2gpp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2gpp
Deposition date deposition_date2006-04-18
Structure title titleEstrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716
Keywords keywordsEstrogen related receptor, ERR, ERRg, ESRRG, Nuclear Receptor, Steroid Receptor, RIP140, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier23.72
Radius of gyration Rg (electron density) rg_electron22.66
Forward intensity I(0) i043541000.00
Molecular weight molecular_weight53643.0 kDa
Excluded volume excluded_volume68244 ų
Envelope volume envelope_volume80589 ų
Hydration-shell volume shell_volume28807 ų
Envelope diameter envelope_diameter76.2
Shell Rg shell_rg30.35
Envelope Rg envelope_rg22.84
Shape Rg shape_rg22.67
Total Rg total_rg23.54
Total atoms total_atoms3766
Residues n_residues473
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 dmax73.6
Rg (real space) rg_real23.57
Rg uncertainty (real space) rg_real_error0.31
I(0) (real space) i0_real4.3540e+07
I(0) uncertainty (real space) i0_real_error5.4980e+05
Rg (reciprocal space) rg_reciprocal23.61
I(0) (reciprocal space) i0_reciprocal43540000.0000
Solution quality estimate total_estimate0.9018
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary29.9
Skewness Skewness skewness0.161
Kurtosis Kurtosis kurtosis-0.448
Angular range angular_range— – 0.3350 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha12060000.0000
Real-space data points n_real_points65
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.990; Smooth: 0.984

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2gppa_
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
Domain ID domain_idd2gppb_
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 (2 domains)

Domain ID domain_id2gppA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id2gppB00
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)