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- PDB-8fb2: HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDI... -

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Basic information

Entry
Database: PDB / ID: 8fb2
TitleHUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 8 ANDINDAZOLE ACID BOUND IN H12-POCKET
ComponentsNuclear receptor ROR-gamma
KeywordsDNA BINDING PROTEIN / RORC2 / RORgammat / structure-based design / macrocyclization / topical delivery
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 / 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-XNX / Chem-XO5 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsVajdos, F.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists.
Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, ...Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, A.L. / Knafels, J.D. / Vazquez, M.L. / Berstein, G.
History
DepositionNov 29, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2356
Polymers60,5022
Non-polymers1,7344
Water3,441191
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1183
Polymers30,2511
Non-polymers8672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1183
Polymers30,2511
Non-polymers8672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.600, 97.680, 56.810
Angle α, β, γ (deg.)90.00, 91.43, 90.00
Int Tables number4
Space group name H-MP1211

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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: 30250.811 Da / Num. of mol.: 2 / Mutation: C278S, C345S
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-XO5 / (1R,15S)-16-(cyclopropylacetyl)-5-fluoro-20-methyl-9lambda~6~-thia-1,8,16-triazatricyclo[13.3.1.1~3,7~]icosa-3(20),4,6-triene-9,9-dione


Mass: 437.571 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H32FN3O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-XNX / 4-[1-(2,6-dichlorobenzoyl)-4-fluoro-1H-indazol-3-yl]benzoic acid


Mass: 429.228 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H11Cl2FN2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.18 Å3/Da / Density % sol: 43.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 5.9, 5 mM ammonium sulfate, 300 mM magnesium chloride, 10% N,N-dimethylformamide, and 14% PEG-MME-5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→97.68 Å / Num. obs: 23071 / % possible obs: 99.1 % / Redundancy: 3.3 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.049 / Rrim(I) all: 0.091 / Net I/σ(I): 11.1 / Num. measured all: 76348
Reflection shellResolution: 2.3→2.81 Å / % possible obs: 99.7 % / Redundancy: 3.3 % / Rmerge(I) obs: 0.363 / Num. measured all: 35176 / Num. unique obs: 10525 / CC1/2: 0.891 / Rpim(I) all: 0.233 / Rrim(I) all: 0.433 / Net I/σ(I) obs: 3.7

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Processing

Software
NameClassification
BUSTERrefinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→25.53 Å / Cor.coef. Fo:Fc: 0.9449 / Cor.coef. Fo:Fc free: 0.9255 / SU R Cruickshank DPI: 0.379 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.364 / SU Rfree Blow DPI: 0.227 / SU Rfree Cruickshank DPI: 0.231
RfactorNum. reflection% reflectionSelection details
Rfree0.2299 1195 5.22 %RANDOM
Rwork0.1785 ---
obs0.1812 22889 99.03 %-
Displacement parametersBiso mean: 48.36 Å2
Baniso -1Baniso -2Baniso -3
1--7.203 Å20 Å21.8782 Å2
2--4.2424 Å20 Å2
3---2.9606 Å2
Refine analyzeLuzzati coordinate error obs: 0.269 Å
Refinement stepCycle: 1 / Resolution: 2.3→25.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4068 0 118 191 4377
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.014357HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.965964HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1552SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes98HARMONIC2
X-RAY DIFFRACTIONt_gen_planes710HARMONIC5
X-RAY DIFFRACTIONt_it4357HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.63
X-RAY DIFFRACTIONt_other_torsion18.01
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion520SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4890SEMIHARMONIC4
LS refinement shellResolution: 2.3→2.41 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.2458 152 4.99 %
Rwork0.2039 2894 -
all0.2059 3046 -
obs--99.7 %

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