6xfv

CRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C IN COMPLEX WITH A NOVEL INVERSE AGONIST

Method: X-RAY DIFFRACTION Dmax: 83.9 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 265–508 Not recorded V27 1-(4-{(3S,4S)-4-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-3-methyl-3-phenylpyrrolidine-1-carbonyl}piperidin-1-yl)ethan-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;295 K;1.0M NaAcetate, 0.3 M NaSCN, 0.1M Tris pH 8.0 Resolution 2.15 Å R-free 0.277
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 265–508 Not recorded V27 1-(4-{(3S,4S)-4-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-3-methyl-3-phenylpyrrolidine-1-carbonyl}piperidin-1-yl)ethan-1-one × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;295 K;1.0M NaAcetate, 0.3 M NaSCN, 0.1M Tris pH 8.0 Resolution 2.15 Å R-free 0.277

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 22–265; UniProt 265–508 Author chain B; PDBConstruct 22–265; UniProt 265–508

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 6xfv

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6xfv
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6xfv
Deposition date deposition_date2020-06-16
Structure title titleCRYSTAL STRUCTURE OF RAR-RELATED ORPHAN RECEPTOR C IN COMPLEX WITH A NOVEL INVERSE AGONIST
Keywords keywordsRORGT, NUCLEAR HORMONE RECEPTOR, LIGAND-BINDING DOMAIN, INVERSE AGONIST, TRANSCRIPTION-Agonist complex; TRANSCRIPTION/Agonist
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier26.77
Radius of gyration Rg (electron density) rg_electron25.55
Forward intensity I(0) i044792500.00
Molecular weight molecular_weight51452.0 kDa
Excluded volume excluded_volume64223 ų
Envelope volume envelope_volume82179 ų
Hydration-shell volume shell_volume26775 ų
Envelope diameter envelope_diameter86.4
Shell Rg shell_rg32.86
Envelope Rg envelope_rg25.19
Shape Rg shape_rg25.57
Total Rg total_rg26.36
Total atoms total_atoms3612
Residues n_residues442
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 dmax83.9
Rg (real space) rg_real26.67
Rg uncertainty (real space) rg_real_error0.55
I(0) (real space) i0_real4.4790e+07
I(0) uncertainty (real space) i0_real_error7.0210e+05
Rg (reciprocal space) rg_reciprocal26.70
I(0) (reciprocal space) i0_reciprocal44790000.0000
Solution quality estimate total_estimate0.9072
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.4
Skewness Skewness skewness0.134
Kurtosis Kurtosis kurtosis-0.623
Angular range angular_range— – 0.2950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha8782000.0000
Real-space data points n_real_points60
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.944; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.997; Smooth: 0.961

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (3)

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6xfva_
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_idd6xfvb_
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

8. Citations (1)

9. Files and Curves (10)