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- PDB-5yp5: Crystal structure of RORgamma complexed with SRC2 and compound 5d -

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Basic information

Entry
Database: PDB / ID: 5yp5
TitleCrystal structure of RORgamma complexed with SRC2 and compound 5d
Components
  • Nuclear receptor ROR-gamma
  • SRC2-2 peptide
KeywordsTRANSCRIPTION/INHIBITOR / complex structure / Nuclear receptor ROR / transcription factor / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / 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-modulated transcription factor activity / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / locomotor rhythm / aryl hydrocarbon receptor binding / cellular response to Thyroglobulin triiodothyronine / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / adipose tissue development / lymph node development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / transcription regulator inhibitor activity / cellular response to hormone stimulus / Recycling of bile acids and salts / positive regulation of adipose tissue development / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / nuclear receptor binding / negative regulation of smoothened signaling pathway / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / PPARA activates gene expression / Cytoprotection by HMOX1 / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / DNA-binding transcription repressor activity, RNA polymerase II-specific / RNA polymerase II transcription regulator complex / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Interleukin-4 and Interleukin-13 signaling / transcription regulator complex / Estrogen-dependent gene expression / transcription coactivator activity / DNA-binding transcription factor activity, RNA polymerase II-specific / protein dimerization activity / nuclear body / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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-4CZ / Nuclear receptor ROR-gamma / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsGao, M. / Cai, W. / Chunwa, C.
CitationJournal: ACS Med Chem Lett / Year: 2018
Title: From ROR gamma t Agonist to Two Types of ROR gamma t Inverse Agonists
Authors: Wang, Y. / Cai, W. / Tang, T. / Liu, Q. / Yang, T. / Yang, L. / Ma, Y. / Zhang, G. / Huang, Y. / Song, X. / Orband-Miller, L.A. / Wu, Q. / Zhou, L. / Xiang, Z. / Xiang, J.N. / Leung, S. / ...Authors: Wang, Y. / Cai, W. / Tang, T. / Liu, Q. / Yang, T. / Yang, L. / Ma, Y. / Zhang, G. / Huang, Y. / Song, X. / Orband-Miller, L.A. / Wu, Q. / Zhou, L. / Xiang, Z. / Xiang, J.N. / Leung, S. / Shao, L. / Lin, X. / Lobera, M. / Ren, F.
History
DepositionNov 1, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 4, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: SRC2-2 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8783
Polymers29,3312
Non-polymers5471
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-7 kcal/mol
Surface area11900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.069, 62.069, 154.818
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 28307.824 Da / Num. of mol.: 1 / Fragment: UNP residues 265-507
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET21d / Cell line (production host): BL21 (DE3)
Production host: Escherichia coli-Thermus thermophilus shuttle vector pTRH1T (others)
References: UniProt: P51449
#2: Protein/peptide SRC2-2 peptide


Mass: 1023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596*PLUS
#3: Chemical ChemComp-4CZ / 2-[4-(ethylsulfonyl)phenyl]-N-{5-[2-(2-methylpropyl)benzoyl]-4-phenyl-1,3-thiazol-2-yl}acetamide


Mass: 546.700 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30N2O4S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Ammonium Sulfate, 0.1M Bis-Tris, pH 6.5, 14% (w/v) PEG 8000

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Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 13, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.65→57.6 Å / Num. obs: 8323 / % possible obs: 92.6 % / Redundancy: 7.3 % / Net I/σ(I): 23.4
Reflection shellResolution: 2.65→2.718 Å

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
HKL-2000data scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.65→57.61 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.903 / SU B: 22.374 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 3.946 / ESU R Free: 0.348 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25324 417 4.8 %RANDOM
Rwork0.20613 ---
obs0.20822 8323 93.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.949 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20 Å2
2--0.11 Å20 Å2
3----0.22 Å2
Refinement stepCycle: 1 / Resolution: 2.65→57.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 38 26 2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212090
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.041.9712822
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2555249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg26.65823.01193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.61915367
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6611514
X-RAY DIFFRACTIONr_chiral_restr0.0610.2314
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211557
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.2981.51250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.61822004
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.023840
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7854.5818
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.65→2.718 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.308 28 -
Rwork0.248 615 -
obs--94.98 %

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