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- PDB-6b33: Structure of RORgt in complex with a novel inverse agonist 3 -

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Basic information

Entry
Database: PDB / ID: 6b33
TitleStructure of RORgt in complex with a novel inverse agonist 3
ComponentsNuclear receptor ROR-gamma
Keywordssignaling protein/antagonist / Complex / inverse agonist / Nuclear Hormone Receptor / signaling protein-antagonist complex
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 / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / 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 / 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 / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / 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-CF7 / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.48 Å
AuthorsSkene, R.J. / Hoffman, I. / Snell, G.
CitationJournal: Chemmedchem / Year: 2019
Title: Design and Synthesis of Conformationally Constrained ROR gamma t Inverse Agonists.
Authors: Sato, A. / Fukase, Y. / Kono, M. / Ochida, A. / Oda, T. / Sasaki, Y. / Ishii, N. / Tomata, Y. / Fukumoto, S. / Imai, Y.N. / Uga, K. / Shibata, A. / Yamasaki, M. / Nakagawa, H. / Shirasaki, M. ...Authors: Sato, A. / Fukase, Y. / Kono, M. / Ochida, A. / Oda, T. / Sasaki, Y. / Ishii, N. / Tomata, Y. / Fukumoto, S. / Imai, Y.N. / Uga, K. / Shibata, A. / Yamasaki, M. / Nakagawa, H. / Shirasaki, M. / Skene, R. / Hoffman, I. / Sang, B.C. / Snell, G. / Shirai, J. / Yamamoto, S.
History
DepositionSep 20, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 21, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 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

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)51,9034
Polymers50,7732
Non-polymers1,1302
Water2,252125
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9512
Polymers25,3861
Non-polymers5651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,9512
Polymers25,3861
Non-polymers5651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.211, 99.211, 126.332
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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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: 25386.354 Da / Num. of mol.: 2
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-CF7 / (2R)-N~2~-(3-chloro-4-cyanophenyl)-N~4~-[3-(cyclopropylmethyl)-2,4-dioxo-1-(propan-2-yl)-1,2,3,4-tetrahydroquinazolin-6-yl]morpholine-2,4-dicarboxamide


Mass: 565.020 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H29ClN6O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 3.53 Å3/Da / Density % sol: 65.2 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 1.6M Sodium Formate, 3% MPD, and 100 mM HEPES (pH 7.5)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.48→50 Å / Num. obs: 24960 / % possible obs: 100 % / Redundancy: 8.1 % / Rmerge(I) obs: 0.075 / Χ2: 1.004 / Net I/σ(I): 11.1 / Num. measured all: 202120
Reflection shell
Resolution (Å)Redundancy (%)Num. unique obsΧ2Diffraction-ID% possible allRmerge(I) obs
2.48-2.527.912470.9211100
2.52-2.578.112220.9851100
2.57-2.628.212720.9781100
2.62-2.678.212501.021100
2.67-2.738.212161.03911000.877
2.73-2.798.212461.02711000.697
2.79-2.868.212511.02911000.533
2.86-2.948.212371.02311000.424
2.94-3.038.212451.04411000.359
3.03-3.128.212451.00711000.284
3.12-3.248.212411.01211000.213
3.24-3.378.212440.99111000.139
3.37-3.528.212530.99811000.109
3.52-3.78.21232111000.079
3.7-3.948.212620.99911000.062
3.94-4.248.112471.00311000.058
4.24-4.677.912461.00411000.058
4.67-5.347.812631.00211000.057
5.34-6.737.61260111000.046
6.73-50812810.991199.50.028

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMACrefinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.48→39.01 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / WRfactor Rfree: 0.2417 / WRfactor Rwork: 0.1977 / FOM work R set: 0.7991 / SU B: 19.779 / SU ML: 0.207 / SU R Cruickshank DPI: 0.3215 / SU Rfree: 0.2407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.322 / ESU R Free: 0.241 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2391 1268 5.1 %RANDOM
Rwork0.193 ---
obs0.1953 23651 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.19 Å2 / Biso mean: 66.518 Å2 / Biso min: 43.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20.04 Å2-0 Å2
2--0.08 Å20 Å2
3----0.27 Å2
Refinement stepCycle: final / Resolution: 2.48→39.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3524 0 80 125 3729
Biso mean--59.14 66.66 -
Num. residues----436
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0193710
X-RAY DIFFRACTIONr_bond_other_d0.0020.023484
X-RAY DIFFRACTIONr_angle_refined_deg1.4121.9745007
X-RAY DIFFRACTIONr_angle_other_deg0.94637981
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8945440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.65723.056180
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615671
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6371532
X-RAY DIFFRACTIONr_chiral_restr0.0720.2541
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024185
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02905
LS refinement shellResolution: 2.483→2.547 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 98 -
Rwork0.307 1755 -
all-1853 -
obs--100 %
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)
12.5275-1.7904-0.92264.41042.26252.2451-0.0622-0.02060.0864-0.1035-0.0384-0.0515-0.1236-0.05640.10060.0978-0.0011-0.03830.05180.02570.0437-31.439118.0873.479
25.54851.0276-2.85411.3652-0.50092.68780.0895-0.0915-0.026-0.048-0.05270.0603-0.23960.1589-0.03680.11250.01560.00360.0353-0.01420.013-34.921120.115-31.28
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A265 - 482
2X-RAY DIFFRACTION1A1000
3X-RAY DIFFRACTION2B265 - 482
4X-RAY DIFFRACTION2B1000

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