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- PDB-9vnx: Crystal Structure of the mutant ROR gamma LBD With Compound 28 -

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Basic information

Entry
Database: PDB / ID: 9vnx
TitleCrystal Structure of the mutant ROR gamma LBD With Compound 28
Components(Nuclear receptor ...) x 2
KeywordsNUCLEAR PROTEIN / nuclear receptor / agonist
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 / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / labyrinthine layer morphogenesis ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated 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 / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / negative regulation of thymocyte apoptotic process / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / regulation of fat cell differentiation / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / adipose tissue development / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / lymph node development / response to retinoic acid / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / estrogen receptor signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / 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 / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / circadian regulation of gene expression / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / 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 / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / response to estradiol / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / nuclear body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / 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 ROR / Retinoid-related orphan receptors, DNA-binding domain / Nuclear receptor coactivator 1 / 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 / 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
Similarity search - Domain/homology
: / ACETATE ION / Nuclear receptor ROR-gamma / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsAkai, S. / Nomura, A. / Yamaguchi, K. / Adachi, T.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: A Concise and Modular Approach to Generate Novel ROR gamma Agonists.
Authors: Fukuda, S. / Ikenogami, T. / Otake, K. / Miwa, S. / Maeda, K. / Yamashita, T. / Inami, T. / Yokota, M. / Lu, Y. / Suma, A. / Hirono, Y. / Ogawa, N. / Inoue, T. / Harada, K. / Yamaguchi, K. / ...Authors: Fukuda, S. / Ikenogami, T. / Otake, K. / Miwa, S. / Maeda, K. / Yamashita, T. / Inami, T. / Yokota, M. / Lu, Y. / Suma, A. / Hirono, Y. / Ogawa, N. / Inoue, T. / Harada, K. / Yamaguchi, K. / Akai, S. / Nomura, A. / Adachi, T. / Terawaki, T. / Suzukawa, A. / Kitamoto, M. / Tanimoto, M. / Noguchi, T. / Hata, T. / Kawahara, I. / Iwamoto, K. / Kondo, K. / Kitagawa, Y. / Naka, Y. / Crowe, P. / Tao, H. / Fenn, M. / Thacher, S. / Oba, M. / Shiozaki, M.
History
DepositionJul 1, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 30, 2025Provider: repository / Type: Initial release
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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 coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3477
Polymers31,5302
Non-polymers8175
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-2 kcal/mol
Surface area12500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.664, 61.664, 155.779
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

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Nuclear receptor ... , 2 types, 2 molecules AB

#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: 29754.301 Da / Num. of mol.: 1 / Fragment: UNP residues 261-518 / Mutation: K469A/R473A
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 Nuclear receptor coactivator 1 / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal ...NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 1776.072 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15788, histone acetyltransferase

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Non-polymers , 4 types, 154 molecules

#3: Chemical ChemComp-A1MAM / (2~{R})-~{N}-[5-(5-cyano-6-propan-2-yloxy-pyridin-3-yl)-1-(trifluoromethyl)pyrazol-3-yl]-1-ethanoyl-4-propan-2-ylsulfonyl-piperazine-2-carboxamide


Mass: 571.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28F3N7O5S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.35 Å3/Da / Density % sol: 47.62 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 0.1M sodium acetate (pH 7.0), 3.5M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 2, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.93→61.66 Å / Num. obs: 22946 / % possible obs: 98.3 % / Redundancy: 26.5 % / Biso Wilson estimate: 25.29 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.184 / Rpim(I) all: 0.036 / Rrim(I) all: 0.188 / Net I/σ(I): 17.3
Reflection shellResolution: 1.93→1.98 Å / Rmerge(I) obs: 1.847 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 1473 / CC1/2: 0.792 / Rpim(I) all: 0.352 / Rrim(I) all: 1.881

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→57.34 Å / SU ML: 0.1884 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.7815
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2182 1115 4.86 %
Rwork0.1875 21808 -
obs0.1891 22923 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 28.23 Å2
Refinement stepCycle: LAST / Resolution: 1.93→57.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2051 0 55 149 2255
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00232197
X-RAY DIFFRACTIONf_angle_d0.47162968
X-RAY DIFFRACTIONf_chiral_restr0.0339319
X-RAY DIFFRACTIONf_plane_restr0.0036379
X-RAY DIFFRACTIONf_dihedral_angle_d11.5851826
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.93-2.020.23951180.21652632X-RAY DIFFRACTION96.56
2.02-2.120.26391400.19832658X-RAY DIFFRACTION96.88
2.12-2.260.22511470.18492627X-RAY DIFFRACTION97.09
2.26-2.430.22541240.17832688X-RAY DIFFRACTION97.54
2.43-2.680.21731310.18192720X-RAY DIFFRACTION97.7
2.68-3.060.21951440.1922726X-RAY DIFFRACTION98.09
3.06-3.860.22741440.1812796X-RAY DIFFRACTION98.66
3.86-57.340.19941670.18872961X-RAY DIFFRACTION99.08
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)
14.35440403674.773462975765.50812646786.478200193226.434653003018.42644737914-0.0395931567175-0.2296869330960.09351236310450.09807228920690.07367260359560.4036910138940.463960220256-0.869085305165-0.00236210329290.257906038372-0.05088727304090.01793100863310.3126963032770.0463035525170.278347425534-15.691521688512.731407587814.1265326826
24.29437552581-0.3299748473461.536901284813.570141751810.7120492665042.21121946459-0.00369094071382-0.2525544917230.5799662774780.17212455446-0.1147390516180.0647880582485-0.231216965177-0.1818043854950.1422723407440.2794477660570.05993921665750.01337785864390.204684793353-0.03314816294920.2017993985631.2733413363234.713690501329.4289220475
39.021240964335.776983501663.089362027644.444484325312.457099846112.133906128260.47128753694-0.5380921957580.2124402751450.388986170246-0.4271252949250.1618486150730.240988977037-0.181123818962-0.04567804263290.2067506508260.00486130732406-0.01151281218750.1499160732330.03388660166330.1319187800935.4515785674519.010230892629.3867763155
42.73472426673-1.41372078243-0.4244057824734.932521229741.581949630543.112007738190.04146336737820.111698469459-0.2379862552560.32913755333-0.0960176409317-0.1646457842330.2805907571860.08318877979760.03247794714550.202934313380.00709470559332-0.03634502731410.217945645311-0.01509567534060.1558864711150.15466074380610.496818332118.5660066569
51.699719465671.195616063380.7610696572461.872959346471.001234874851.25782446481-0.1157227903790.1003562142910.222727210015-0.1440398383990.04526637324070.0377230926392-0.287105490087-0.03511772257650.08446038086490.26980724050.00339308040865-0.02218835534750.1616068856810.03268733657290.1847771098012.9730406878629.460072558118.1895968307
66.58556912477-4.41784685852.842528168625.34389327177-1.962401530611.806012384750.2453993384730.388218906473-0.561997883973-0.383187219659-0.06681539755970.3691461836170.2745753135460.0472321600749-0.1405168937790.2098593365580.00362220185766-0.007921409884360.219397615296-0.00725256520610.16028766254-4.582539294037.922870317346.96456178199
71.713953336422.928453376690.5791809774825.159995560321.688119190723.37718379735-0.386367349931-0.273725958264-0.254213900151-0.3299734478850.13814875038-0.250028510459-0.05890881652410.7239275362250.2578342601010.263684737239-0.0123706359062-0.04567289463870.3570607386260.07112777821470.224583742087-5.2663711222424.41387432113.12246792832
83.170335019981.683550612990.9807921886650.995027620556-0.2935844779886.38649849613-0.01316703965760.219381495837-0.130500814392-0.1291496653050.051532173994-0.2821487161640.1187331738780.441599160455-0.07156575412690.2349772603890.05588911082780.009392678470160.127870261581-0.01849578312480.21897318968816.089744069816.807492507325.021025108
92.564476938561.505757025113.05561805356.05497634271.288228545864.882404401850.418097303541-0.92824014451-1.43581340370.898668517433-0.0243616585242-0.5823594849131.38166801986-0.310195463362-0.2589359833030.70376910836-0.0799144784302-0.05531729037740.3705133899660.07661859405710.4295564040671.480632141943.2323588382629.8675732201
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 266 through 284 )AA266 - 2841 - 19
22chain 'A' and (resid 285 through 312 )AA285 - 31220 - 47
33chain 'A' and (resid 313 through 337 )AA313 - 33748 - 72
44chain 'A' and (resid 338 through 368 )AA338 - 36873 - 103
55chain 'A' and (resid 369 through 425 )AA369 - 425104 - 160
66chain 'A' and (resid 426 through 456 )AA426 - 456161 - 191
77chain 'A' and (resid 457 through 470 )AA457 - 470192 - 205
88chain 'A' and (resid 471 through 507 )AA471 - 507206 - 242
99chain 'B' and (resid 688 through 696 )BG688 - 6961 - 9

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