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- PDB-4wpf: Crystal structure of RORc in complex with a phenyl sulfonamide agonist -

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Basic information

Entry
Database: PDB / ID: 4wpf
TitleCrystal structure of RORc in complex with a phenyl sulfonamide agonist
Components
  • Nuclear receptor ROR-gamma
  • RHKILHRLLQEGSPS
KeywordsTRANSCRIPTION / ROR / RORc / RORg / nuclear receptor
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-3SN / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.202 Å
AuthorsKiefer, J.R. / Wallweber, H.A. / de Leon Boenig, G. / Hymowitz, S.G.
CitationJournal: Acs Med.Chem.Lett. / Year: 2015
Title: Minor Structural Change to Tertiary Sulfonamide RORc Ligands Led to Opposite Mechanisms of Action.
Authors: Rene, O. / Fauber, B.P. / de Leon Boenig, G. / Burton, B. / Eidenschenk, C. / Everett, C. / Gobbi, A. / Hymowitz, S.G. / Johnson, A.R. / Kiefer, J.R. / Liimatta, M. / Lockey, P. / Norman, M. ...Authors: Rene, O. / Fauber, B.P. / de Leon Boenig, G. / Burton, B. / Eidenschenk, C. / Everett, C. / Gobbi, A. / Hymowitz, S.G. / Johnson, A.R. / Kiefer, J.R. / Liimatta, M. / Lockey, P. / Norman, M. / Ouyang, W. / Wallweber, H.A. / Wong, H.
History
DepositionOct 18, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2015Group: Database references
Revision 1.2Dec 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _refine_hist.number_atoms_total / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,2656
Polymers64,3744
Non-polymers8912
Water4,792266
1
A: Nuclear receptor ROR-gamma
B: RHKILHRLLQEGSPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6333
Polymers32,1872
Non-polymers4461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area12610 Å2
MethodPISA
2
D: Nuclear receptor ROR-gamma
E: RHKILHRLLQEGSPS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6333
Polymers32,1872
Non-polymers4461
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1030 Å2
ΔGint-7 kcal/mol
Surface area12710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.692, 61.692, 155.232
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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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: 30825.486 Da / Num. of mol.: 2 / Fragment: UNP residues 262-509
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: Protein/peptide RHKILHRLLQEGSPS


Mass: 1361.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-3SN / N-[4-(4-acetylpiperazin-1-yl)-2-fluorobenzyl]-N-cyclobutylbenzenesulfonamide


Mass: 445.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H28FN3O3S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 266 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 6.5
Details: 0.2M sodium formate, 0.1M Bis Tris propane (pH 6.5), and 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.546
11K, H, -L20.454
ReflectionResolution: 2.2→40 Å / Num. obs: 28529 / % possible obs: 97.4 % / Redundancy: 2.8 % / Rmerge(I) obs: 0.11 / Χ2: 0.878 / Net I/av σ(I): 8.262 / Net I/σ(I): 6 / Num. measured all: 79558
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.2-2.242.30.75412120.65785.5
2.24-2.282.50.5814300.99795.3
2.28-2.322.70.60813710.66997.1
2.32-2.372.70.54414620.65297.1
2.37-2.422.70.45514200.66797.9
2.42-2.482.70.44614230.69898.1
2.48-2.542.70.43514290.72398
2.54-2.612.70.38814180.76498.1
2.61-2.692.70.32914600.75398.2
2.69-2.772.80.31914230.81898.1
2.77-2.872.70.2414520.8298.8
2.87-2.992.80.19814280.86598.1
2.99-3.122.80.17314370.96698.6
3.12-3.292.90.14314631.11998.7
3.29-3.492.90.10514481.13498.7
3.49-3.762.90.0814581.17799.2
3.76-4.1430.05714541.12399.2
4.14-4.7430.04914671.13599.2
4.74-5.9730.04614380.87798.4
5.97-403.20.02614360.7195

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Processing

Software
NameVersionClassificationNB
REFMAC5.6.0117refinement
PDB_EXTRACT3.15data extraction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.202→35 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.924 / SU B: 8.265 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.21 / ESU R Free: 0.058 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2271 2201 10.3 %RANDOM
Rwork0.1749 19107 --
obs0.1802 41797 72.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 62.94 Å2 / Biso mean: 24.944 Å2 / Biso min: 14.4 Å2
Baniso -1Baniso -2Baniso -3
1-3.29 Å20 Å20 Å2
2--3.29 Å20 Å2
3----6.58 Å2
Refinement stepCycle: final / Resolution: 2.202→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4215 0 62 266 4543
Biso mean--47.44 33.44 -
Num. residues----513
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0194390
X-RAY DIFFRACTIONr_bond_other_d0.0010.023004
X-RAY DIFFRACTIONr_angle_refined_deg0.8341.9685921
X-RAY DIFFRACTIONr_angle_other_deg0.76437277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2235514
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.07623.056216
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.75115799
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.741536
X-RAY DIFFRACTIONr_chiral_restr0.0450.2642
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024800
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02932
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.273 13 -
Rwork0.21 104 -
all-117 -
obs--5.45 %
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)
10.96090.37270.13251.18960.46690.98070.05380.01060.01760.016-0.05090.0158-0.0508-0.0228-0.00290.02590.00890.00150.02490.01190.008410.350561.103310.947
23.7133.46180.261311.78613.854910.0743-0.22720.531-0.3909-0.48750.2891-0.73560.20770.5328-0.06180.1214-0.00350.06580.2637-0.02370.283227.593758.0542-0.7195
31.0658-0.4672-0.25391.30970.54791.0270.04420.0302-0.0393-0.051-0.04370.0410.0296-0.0397-0.00050.0286-0.0052-0.00260.02610.01110.0096-20.494831.45918.3756
42.4873-2.7631-0.72285.8094-1.50417.5066-0.1174-0.76310.11570.61170.366-0.7757-0.25820.5674-0.24860.2163-0.0333-0.07940.37980.0350.3514-3.202834.589320.0762
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A243 - 488
2X-RAY DIFFRACTION2B6 - 16
3X-RAY DIFFRACTION3D243 - 488
4X-RAY DIFFRACTION4E6 - 16

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