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- PDB-6lo9: Crystal structure of RORgammat with ligand C46D bound -

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Basic information

Entry
Database: PDB / ID: 6lo9
TitleCrystal structure of RORgammat with ligand C46D bound
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / RORgammat proteins / ligand binding domain / agonist
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
Similarity search - Domain/homology
Chem-ENU / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8600494706 Å
AuthorsFeng, Y. / Shijie, C.
CitationJournal: To Be Published
Title: Crystal structure of RORgammat with ligand C46D bound
Authors: Feng, Y. / Shijie, C.
History
DepositionJan 4, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5992
Polymers32,0801
Non-polymers5191
Water2,702150
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.583, 61.583, 155.507
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2

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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: 32080.035 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449
#2: Chemical ChemComp-ENU / 6-cyclohexyloxy-9-ethyl-~{N}-[(4-ethylsulfonylphenyl)methyl]carbazole-3-carboxamide


Mass: 518.667 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H34N2O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.3 Å3/Da / Density % sol: 46.47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 8% PEG4000, 0.4M NaCl, 0.1M PIPES, pH6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.987 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.86→27.76 Å / Num. obs: 26005 / % possible obs: 100 % / Redundancy: 3.26 % / Biso Wilson estimate: 27.79 Å2 / CC1/2: 0.995 / Net I/σ(I): 3.26
Reflection shellResolution: 1.86→1.927 Å / Rmerge(I) obs: 0.934 / Mean I/σ(I) obs: 3 / Num. unique obs: 2545 / CC1/2: 0.999 / Rpim(I) all: 0.233 / Rrim(I) all: 0.963 / Χ2: 0.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XYZ

1xyz


Resolution: 1.8600494706→27.76 Å / SU ML: 0.164430888288 / Cross valid method: FREE R-VALUE / σ(F): 1.38102327631 / Phase error: 20.7245195949
RfactorNum. reflection% reflection
Rfree0.226875138836 1350 5.19190831475 %
Rwork0.192641806531 --
obs0.194340809936 26002 99.9423453896 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 31.8869180174 Å2
Refinement stepCycle: LAST / Resolution: 1.8600494706→27.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2099 0 37 150 2286
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.007105695711552232
X-RAY DIFFRACTIONf_angle_d1.280159568133018
X-RAY DIFFRACTIONf_chiral_restr0.0465933142627322
X-RAY DIFFRACTIONf_plane_restr0.00408406259595385
X-RAY DIFFRACTIONf_dihedral_angle_d17.66219440391334
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.861-1.92650.2647378744731380.2274128119922407X-RAY DIFFRACTION100
1.9265-2.00360.283541722351260.2160723526632400X-RAY DIFFRACTION99.9604273843
2.0036-2.09480.2556138319261360.2010010264522420X-RAY DIFFRACTION100
2.0948-2.20520.2376894306371320.1952810763962437X-RAY DIFFRACTION99.9610894942
2.2052-2.34340.2305885442181330.1938044973012413X-RAY DIFFRACTION100
2.3434-2.52420.2415189141341350.1963560339992442X-RAY DIFFRACTION100
2.5242-2.77820.2645961375291410.2028026490782461X-RAY DIFFRACTION100
2.7782-3.17990.2298805035611420.1979535720432465X-RAY DIFFRACTION100
3.1799-4.00520.1988624769481140.1808582891522539X-RAY DIFFRACTION100
4.0052-27.760.2037125706181530.1852411588492668X-RAY DIFFRACTION99.5412844037

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