6e3g

Structure of RORgt in complex with a novel agonist.

Method: X-RAY DIFFRACTION Dmax: 92.8 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 263–507 Not recorded co-activator peptide × 1 EDO 1,2-ETHANEDIOL × 1 HOJ (5R)-6-acetyl-2-methoxy-N-{4-[(2-methoxyphenyl)methoxy]phenyl}-5,6,7,8-tetrahydro-1,6-naphthyridine-5-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;20% PEG3350, 0.2M AmmNitrate, 0.1M Citrate pH 6.0 Resolution 2.10 Å R-free 0.243
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 263–507 Not recorded co-activator peptide × 1 EDO 1,2-ETHANEDIOL × 1 HOJ (5R)-6-acetyl-2-methoxy-N-{4-[(2-methoxyphenyl)methoxy]phenyl}-5,6,7,8-tetrahydro-1,6-naphthyridine-5-carboxamide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;291 K;20% PEG3350, 0.2M AmmNitrate, 0.1M Citrate pH 6.0 Resolution 2.10 Å R-free 0.243

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 1–245; UniProt 263–507 Author chain B; PDBConstruct 1–245; UniProt 263–507

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 6e3g

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6e3g
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6e3g
Deposition date deposition_date2018-07-13
Structure title titleStructure of RORgt in complex with a novel agonist.
Keywords keywordsNuclear hormone receptor, agonist, NUCLEAR PROTEIN, nuclear protein-agonist complex; nuclear protein/agonist
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier28.76
Radius of gyration Rg (electron density) rg_electron27.97
Forward intensity I(0) i057134200.00
Molecular weight molecular_weight60080.0 kDa
Excluded volume excluded_volume75694 ų
Envelope volume envelope_volume93101 ų
Hydration-shell volume shell_volume29098 ų
Envelope diameter envelope_diameter98.1
Shell Rg shell_rg33.93
Envelope Rg envelope_rg27.96
Shape Rg shape_rg27.96
Total Rg total_rg28.61
Total atoms total_atoms4228
Residues n_residues506
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 dmax92.8
Rg (real space) rg_real28.88
Rg uncertainty (real space) rg_real_error0.71
I(0) (real space) i0_real5.7130e+07
I(0) uncertainty (real space) i0_real_error8.4190e+05
Rg (reciprocal space) rg_reciprocal28.83
I(0) (reciprocal space) i0_reciprocal57130000.0000
Solution quality estimate total_estimate0.8685
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.7
Skewness Skewness skewness0.464
Kurtosis Kurtosis kurtosis-0.394
Angular range angular_range— – 0.2750 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha14950000.0000
Real-space data points n_real_points56
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.871; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.767

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd6e3ga_
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_idd6e3gb_
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_id6e3gA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id6e3gB00
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)