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- PDB-5k6e: Crystal structure of Retinoic acid receptor-related orphan recept... -

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Basic information

Entry
Database: PDB / ID: 5k6e
TitleCrystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with SBI0654919
ComponentsNuclear receptor ROR-gamma
Keywordstranscription/transcription inhibitor / double helix / signaling protein-inhibitor complex / transcription-transcription inhibitor complex
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-6QP / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
Model detailsROR gamma ligand binding domain in complex with SBI0654919
AuthorsLu, J. / Rastinejad, F.
CitationJournal: To be published
Title: Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with SBI0654919
Authors: Lu, J. / Rastinejad, F.
History
DepositionMay 24, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,4324
Polymers57,4432
Non-polymers9902
Water28816
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2162
Polymers28,7211
Non-polymers4951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,2162
Polymers28,7211
Non-polymers4951
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1720 Å2
ΔGint-3 kcal/mol
Surface area22540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.667, 139.930, 120.048
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 28721.289 Da / Num. of mol.: 2 / Fragment: ligand binding domain, unp residues 265-498
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P51449
#2: Chemical ChemComp-6QP / 2-chloranyl-6-fluoranyl-~{N}-[(2~{R})-4-(4-fluorophenyl)sulfonyl-2-(hydroxymethyl)-2,3-dihydro-1,4-benzoxazin-6-yl]benzamide


Mass: 494.896 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H17ClF2N2O5S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.54 Å3/Da / Density % sol: 72.89 % / Mosaicity: 0.392 °
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.4M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2014
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 23231 / % possible obs: 91.7 % / Redundancy: 3.3 % / Biso Wilson estimate: 38.67 Å2 / Rmerge(I) obs: 0.126 / Net I/av σ(I): 9.45 / Net I/σ(I): 8.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.8-2.852.50.337179.8
2.85-2.92.60.339180.5
2.9-2.962.70.365183.7
2.96-3.022.80.314184.1
3.02-3.082.90.336185.8
3.08-3.1530.332186.4
3.15-3.2330.284189.5
3.23-3.323.10.253192
3.32-3.423.20.214194
3.42-3.533.20.201194.7
3.53-3.653.30.175194.6
3.65-3.83.40.139196.8
3.8-3.973.40.129197.5
3.97-4.183.60.112197.2
4.18-4.443.60.103197.9
4.44-4.793.70.096197.3
4.79-5.273.70.102196.8
5.27-6.033.80.117196.7
6.03-7.593.70.101195.5
7.59-503.60.098193

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3L0L

3l0l


Resolution: 2.8→42.161 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.86
RfactorNum. reflection% reflection
Rfree0.2593 1043 5.11 %
Rwork0.2091 --
obs0.2115 20409 80.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 125.61 Å2 / Biso mean: 37.73 Å2 / Biso min: 6.56 Å2
Refinement stepCycle: final / Resolution: 2.8→42.161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3759 0 66 16 3841
Biso mean--45.96 30.66 -
Num. residues----460
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083907
X-RAY DIFFRACTIONf_angle_d1.2625265
X-RAY DIFFRACTIONf_chiral_restr0.044569
X-RAY DIFFRACTIONf_plane_restr0.005667
X-RAY DIFFRACTIONf_dihedral_angle_d21.3961484
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7789-2.92540.33591090.2521914202357
2.9254-3.10860.29371310.24652211234266
3.1086-3.34860.31571510.25042472262373
3.3486-3.68540.25731590.21192794295382
3.6854-4.21820.24161600.19383222338294
4.2182-5.31280.2391660.1923355352197
5.3128-42.16570.23481670.20023398356595

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