3b0w

Crystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin

Method: X-RAY DIFFRACTION Dmax: 84.2 Å Quality: EXCELLENT

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

Nuclear receptor ROR-gamma

Homo sapiens

UniProt P51449

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 monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 265–507 Fragment:LIGAND-BINDING DOMAIN, UNP residues 265-507 DGX DIGOXIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;1.2M Na formate, 3% (v/v) 2-Methyl-2,4-pentanediol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.20 Å R-free 0.249
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 265–507 Fragment:LIGAND-BINDING DOMAIN, UNP residues 265-507 DGX DIGOXIN × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;295 K;1.2M Na formate, 3% (v/v) 2-Methyl-2,4-pentanediol, 0.1M HEPES, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 295K Resolution 2.20 Å R-free 0.249

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.

161 other PDB entries and 266 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RORG_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–243; UniProt 265–507 Author chain B; PDBConstruct 1–243; UniProt 265–507

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 3b0w

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3b0w
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3b0w
Deposition date deposition_date2011-06-17
Structure title titleCrystal structure of the orphan nuclear receptor ROR(gamma)t ligand-binding domain in complex with digoxin
Keywords keywordsTHREE-LAYERED ALPHA HELICAL SANDWICH, ORPHAN NUCLEAR RECEPTOR, LIGAND-BINDING DOMAIN, ANTAGONIST, TRANSCRIPTION-INHIBITOR complex; TRANSCRIPTION/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.85
Radius of gyration Rg (electron density) rg_electron25.59
Forward intensity I(0) i044329800.00
Molecular weight molecular_weight51685.0 kDa
Excluded volume excluded_volume64852 ų
Envelope volume envelope_volume83130 ų
Hydration-shell volume shell_volume27066 ų
Envelope diameter envelope_diameter86.9
Shell Rg shell_rg32.75
Envelope Rg envelope_rg25.19
Shape Rg shape_rg25.59
Total Rg total_rg26.42
Total atoms total_atoms3626
Residues n_residues432
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 dmax84.2
Rg (real space) rg_real26.73
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real4.4330e+07
I(0) uncertainty (real space) i0_real_error6.7310e+05
Rg (reciprocal space) rg_reciprocal26.77
I(0) (reciprocal space) i0_reciprocal44330000.0000
Solution quality estimate total_estimate0.9083
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary38.5
Skewness Skewness skewness0.112
Kurtosis Kurtosis kurtosis-0.645
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8839000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.998

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3b0wa_
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.123.1.0 — automated matches
Domain ID domain_idd3b0wb_
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.123.1.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id3b0wA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id3b0wB00
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)