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- PDB-4nb6: Crystal structure of the ligand binding domain of RORC with T0901317 -

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Basic information

Entry
Database: PDB / ID: 4nb6
TitleCrystal structure of the ligand binding domain of RORC with T0901317
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION / alpha-helical / transcription factor / nucleus
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / 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 / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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-444 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsHymowitz, S.G. / Boenig-de Leon, G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2013
Title: Structure-based design of substituted hexafluoroisopropanol-arylsulfonamides as modulators of RORc.
Authors: Fauber, B.P. / de Leon Boenig, G. / Burton, B. / Eidenschenk, C. / Everett, C. / Gobbi, A. / Hymowitz, S.G. / Johnson, A.R. / Liimatta, M. / Lockey, P. / Norman, M. / Ouyang, W. / Rene, O. / Wong, H.
History
DepositionOct 22, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2013Group: Database references
Revision 1.2Sep 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)59,0464
Polymers58,0832
Non-polymers9632
Water362
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5232
Polymers29,0421
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5232
Polymers29,0421
Non-polymers4811
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.534, 99.534, 125.777
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.993306, 0.114302, 0.016698), (0.114172, -0.993424, 0.008525), (0.017563, -0.006561, -0.999824)-0.59003, 0.09502, 28.27436

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Components

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


Mass: 29041.543 Da / Num. of mol.: 2 / Fragment: ligand binding domain, UNP residues 262-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1F3, RORC, RORG, RZRG / Plasmid: pET52b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Gold / References: UniProt: P51449
#2: Chemical ChemComp-444 / N-(2,2,2-TRIFLUOROETHYL)-N-{4-[2,2,2-TRIFLUORO-1-HYDROXY-1-(TRIFLUOROMETHYL)ETHYL]PHENYL}BENZENESULFONAMIDE


Mass: 481.333 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H12F9NO3S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 2 / 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: 3.1 Å3/Da / Density % sol: 60.28 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 7
Details: drops were composed of 1uL of RORC-agonist complex (20 mM Trish-HCL pH 7.0, 200 mM NaCl, 4% glycerol, 5 mM DTT) plus 1 uL of well solution (400 mM Na/K tartrate), VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 16526 / Num. obs: 16526 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 9.6 % / Rsym value: 0.094 / Net I/σ(I): 22.8
Reflection shellResolution: 2.85→2.95 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 3 / Num. unique all: 1634 / Rsym value: 0.765 / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3L0L

3l0l


Resolution: 2.85→49.77 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.901 / SU B: 38.724 / SU ML: 0.336 / Cross valid method: THROUGHOUT / ESU R Free: 0.41 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27023 1574 9.9 %RANDOM
Rwork0.21625 ---
all0.22157 16504 --
obs0.22157 14362 96.42 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 79.375 Å2
Baniso -1Baniso -2Baniso -3
1-2.75 Å21.37 Å2-0 Å2
2--2.75 Å2-0 Å2
3----4.12 Å2
Refinement stepCycle: LAST / Resolution: 2.85→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3625 0 62 2 3689
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0193783
X-RAY DIFFRACTIONr_angle_refined_deg0.9811.985116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.575441
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.28623.048187
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.62515698
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6161534
X-RAY DIFFRACTIONr_chiral_restr0.0650.2545
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022806
LS refinement shellResolution: 2.85→2.91 Å / Total num. of bins used: 25
RfactorNum. reflection% reflection
Rfree0.295 83 -
Rwork0.285 725 -
obs--84.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.9111-3.1813-2.24095.86182.25382.55-0.3855-0.22950.03580.74720.29710.17130.4489-0.00910.08840.23850.0484-0.01140.0464-0.02020.075637.44043.9864-2.3195
23.14912.71742.42955.9712.02592.1725-0.40060.0949-0.0182-0.91240.26740.0062-0.4923-0.10010.13310.4589-0.02170.00090.1455-0.10340.092137.69450.693431.2581
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A246 - 464
2X-RAY DIFFRACTION1A501
3X-RAY DIFFRACTION2B246 - 464
4X-RAY DIFFRACTION2B501

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