5nti

Structural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds

Method: X-RAY DIFFRACTION Dmax: 118.2 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 263–518 Fragment:C-terminal domain, ligand binding domain Mutation:C455S ASN-SER-HIS-GLN-LYS-VAL-THR-LEU-LEU-GLN-LEU-LEU-LEU-GLY-HIS-LYS-ASN-GLU-GLU-ASN × 1 C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;14% PEG 3350, 0.04M NaFormate Resolution 2.40 Å R-free 0.233
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 263–518 Fragment:C-terminal domain, ligand binding domain Mutation:C455S ASN-SER-HIS-GLN-LYS-VAL-THR-LEU-LEU-GLN-LEU-LEU-LEU-GLY-HIS-LYS-ASN-GLU-GLU-ASN × 1 C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;14% PEG 3350, 0.04M NaFormate Resolution 2.40 Å R-free 0.233
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 263–518 Fragment:C-terminal domain, ligand binding domain Mutation:C455S ASN-SER-HIS-GLN-LYS-VAL-THR-LEU-LEU-GLN-LEU-LEU-LEU-GLY-HIS-LYS-ASN-GLU-GLU-ASN × 1 C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;14% PEG 3350, 0.04M NaFormate Resolution 2.40 Å R-free 0.233
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 263–518 Fragment:C-terminal domain, ligand binding domain Mutation:C455S ASN-SER-HIS-GLN-LYS-VAL-THR-LEU-LEU-GLN-LEU-LEU-LEU-GLY-HIS-LYS-ASN-GLU-GLU-ASN × 1 C3S CHOLEST-5-EN-3-YL HYDROGEN SULFATE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7;298 K;14% PEG 3350, 0.04M NaFormate Resolution 2.40 Å R-free 0.233

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
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–257; UniProt 263–518 Author chain B; PDBConstruct 2–257; UniProt 263–518 Author chain C; PDBConstruct 2–257; UniProt 263–518 Author chain D; PDBConstruct 2–257; UniProt 263–518

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 5nti

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5nti
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5nti
Deposition date deposition_date2017-04-28
Structure title titleStructural states of RORgt: X-ray elucidation of molecular mechanisms and binding interactions for natural and synthetic compounds
Keywords keywordsnuclear hormone receptor, ligand-binding domain, agonist, signaling protein; SIGNALING PROTEIN
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.77
Radius of gyration Rg (electron density) rg_electron35.07
Forward intensity I(0) i0207229000.00
Molecular weight molecular_weight119210.0 kDa
Excluded volume excluded_volume150700 ų
Envelope volume envelope_volume192570 ų
Hydration-shell volume shell_volume45608 ų
Envelope diameter envelope_diameter127.6
Shell Rg shell_rg41.44
Envelope Rg envelope_rg35.00
Shape Rg shape_rg35.08
Total Rg total_rg35.51
Total atoms total_atoms8384
Residues n_residues1011
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 dmax118.2
Rg (real space) rg_real35.76
Rg uncertainty (real space) rg_real_error0.94
I(0) (real space) i0_real2.0720e+08
I(0) uncertainty (real space) i0_real_error3.3920e+06
Rg (reciprocal space) rg_reciprocal35.77
I(0) (reciprocal space) i0_reciprocal207200000.0000
Solution quality estimate total_estimate0.8878
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary40.3
Skewness Skewness skewness0.302
Kurtosis Kurtosis kurtosis-0.424
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha80040000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.896; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.866

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd5ntia_
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_idd5ntib_
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_idd5ntic_
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_idd5ntid_
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 (4 domains)

Domain ID domain_id5ntiA00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5ntiB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5ntiC00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology565 — Retinoid X Receptor
Homologous superfamily homologous superfamily10 — Retinoid X Receptor
Domain ID domain_id5ntiD00
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)