5iz0

RORgamma in complex with agonist BIO592 and Coactivator EBI96

Method: X-RAY DIFFRACTION Dmax: 117.7 Å Quality: GOOD

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 238–497 Fragment:Ligand Binding Domain GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN × 1 6F1 N-(4-ethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide × 1 CL CHLORIDE ION × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;0.1M HEPES pH 8.0 0.2M NaCl 25% PEG3350 Resolution 2.63 Å R-free 0.255
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 238–497 Fragment:Ligand Binding Domain GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN × 1 6F1 N-(4-ethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide × 1 CL CHLORIDE ION × 6 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;0.1M HEPES pH 8.0 0.2M NaCl 25% PEG3350 Resolution 2.63 Å R-free 0.255
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 238–497 Fragment:Ligand Binding Domain GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN × 1 6F1 N-(4-ethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide × 1 CL CHLORIDE ION × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;0.1M HEPES pH 8.0 0.2M NaCl 25% PEG3350 Resolution 2.63 Å R-free 0.255
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 238–497 Fragment:Ligand Binding Domain GLU-PHE-PRO-TYR-LEU-LEU-SER-LEU-LEU-GLY-GLU-VAL-SER-PRO-GLN × 1 6F1 N-(4-ethyl-3-oxo-3,4-dihydro-2H-1,4-benzoxazin-7-yl)-3,4-dimethyl-N-(2,2,2-trifluoroethyl)benzene-1-sulfonamide × 1 CL CHLORIDE ION × 5 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8;298 K;0.1M HEPES pH 8.0 0.2M NaCl 25% PEG3350 Resolution 2.63 Å R-free 0.255

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 264 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RORG_HUMAN
Isoform P51449-2
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 3–263; UniProt 238–497 Author chain B; PDBConstruct 3–263; UniProt 238–497 Author chain D; PDBConstruct 3–263; UniProt 238–497 Author chain G; PDBConstruct 3–263; UniProt 238–497

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 5iz0

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5iz0
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id5iz0
Deposition date deposition_date2016-03-24
Structure title titleRORgamma in complex with agonist BIO592 and Coactivator EBI96
Keywords keywordsRORgamma, Nuclear hormone receptor, Agonist, AF2 helix, IMMUNE SYSTEM; IMMUNE SYSTEM
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.44
Radius of gyration Rg (electron density) rg_electron34.88
Forward intensity I(0) i0217585000.00
Molecular weight molecular_weight119690.0 kDa
Excluded volume excluded_volume150030 ų
Envelope volume envelope_volume190490 ų
Hydration-shell volume shell_volume45343 ų
Envelope diameter envelope_diameter122.0
Shell Rg shell_rg41.22
Envelope Rg envelope_rg34.85
Shape Rg shape_rg34.87
Total Rg total_rg35.36
Total atoms total_atoms8382
Residues n_residues1017
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 dmax117.7
Rg (real space) rg_real35.43
Rg uncertainty (real space) rg_real_error0.66
I(0) (real space) i0_real2.1760e+08
I(0) uncertainty (real space) i0_real_error3.2840e+06
Rg (reciprocal space) rg_reciprocal35.44
I(0) (reciprocal space) i0_reciprocal217600000.0000
Solution quality estimate total_estimate0.8879
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.2
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.451
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha86220000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.889; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.885

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5iz0A00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5iz0B00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5iz0D00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5iz0G00
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)