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- PDB-5w4r: Structure of RORgt bound to a tertiary alcohol -

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Basic information

Entry
Database: PDB / ID: 5w4r
TitleStructure of RORgt bound to a tertiary alcohol
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / RORgt Nuclear Hormone Receptor
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / 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-9WD / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.002 Å
AuthorsSpurlino, J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2017
Title: 6-Substituted quinolines as ROR gamma t inverse agonists.
Authors: Barbay, J.K. / Cummings, M.D. / Abad, M. / Castro, G. / Kreutter, K.D. / Kummer, D.A. / Maharoof, U. / Milligan, C. / Nishimura, R. / Pierce, J. / Schalk-Hihi, C. / Spurlino, J. / Tanis, V.M. ...Authors: Barbay, J.K. / Cummings, M.D. / Abad, M. / Castro, G. / Kreutter, K.D. / Kummer, D.A. / Maharoof, U. / Milligan, C. / Nishimura, R. / Pierce, J. / Schalk-Hihi, C. / Spurlino, J. / Tanis, V.M. / Urbanski, M. / Venkatesan, H. / Wang, A. / Woods, C. / Wolin, R. / Xue, X. / Edwards, J.P. / Fourie, A.M. / Leonard, K.
History
DepositionJun 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6294
Polymers50,4582
Non-polymers1,1702
Water543
1
A: Nuclear receptor ROR-gamma
hetero molecules

B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,6294
Polymers50,4582
Non-polymers1,1702
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_455-x-1,-y,z+1/21
Buried area1400 Å2
ΔGint-10 kcal/mol
Surface area21250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.361, 97.361, 128.218
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: 25229.160 Da / Num. of mol.: 2 / Fragment: UNP residues 265-481
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-9WD / 1-{4-[(R)-(4-chloro-2-methoxy-3-{[4-(1H-pyrazol-1-yl)phenyl]methyl}quinolin-6-yl)(hydroxy)(1-methyl-1H-imidazol-5-yl)methyl]piperidin-1-yl}ethan-1-one


Mass: 585.096 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C32H33ClN6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.48 Å3/Da / Density % sol: 64.62 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: 12% 8K PEG, 100mM HEPES pH7.5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→50 Å / Num. obs: 13833 / % possible obs: 99.8 % / Redundancy: 10.2 % / Biso Wilson estimate: 86.58 Å2 / Rmerge(I) obs: 0.115 / Χ2: 1.63 / Net I/σ(I): 8.8 / Num. measured all: 141311
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsΧ2Diffraction-ID% possible all
3-3.1110.60.480.5781100
3.11-3.2310.70.3270.6421100
3.23-3.3810.60.2250.8751100
3.38-3.5610.50.1761.2071100
3.56-3.7810.20.1411.7731100
3.78-4.079.50.1192.2461100
4.07-4.489.80.122.4751100
4.48-5.1310.70.1112.3961100
5.13-6.4610.40.0992.2171100
6.46-509.20.0892.093197.7

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX(1.10_2155: ???)refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHENIXphasing
RefinementResolution: 3.002→38.122 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 25.11
RfactorNum. reflection% reflection
Rfree0.245 1379 9.99 %
Rwork0.1904 --
obs0.1958 13800 99.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 197.43 Å2 / Biso mean: 85.4671 Å2 / Biso min: 39.44 Å2
Refinement stepCycle: final / Resolution: 3.002→38.122 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3506 0 84 3 3593
Biso mean--73.97 124.86 -
Num. residues----431
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0023667
X-RAY DIFFRACTIONf_angle_d0.4944941
X-RAY DIFFRACTIONf_chiral_restr0.034532
X-RAY DIFFRACTIONf_plane_restr0.002623
X-RAY DIFFRACTIONf_dihedral_angle_d18.6252193
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.0019-3.10920.33511400.239612541394100
3.1092-3.23360.32451380.235112331371100
3.2336-3.38070.30251380.21312411379100
3.3807-3.55880.28451390.195112181357100
3.5588-3.78160.26511350.189812521387100
3.7816-4.07320.23571360.172212411377100
4.0732-4.48260.24041350.165212451380100
4.4826-5.12990.21971430.159812461389100
5.1299-6.4580.2371460.212412451391100
6.458-38.12470.21671290.20041246137598
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)
17.10946.2667-2.16838.8595-3.3193-0.0464-0.1916-0.1443-1.0863-0.7009-0.3068-1.61740.4490.32520.41980.9107-0.025-0.02570.5902-0.04790.6903-28.1863-5.37481.7519
28.79877.3852-1.72356.853-2.97153.0439-0.71920.36850.2454-1.85610.3516-0.6027-0.02590.2481-0.0370.6711-0.04190.06510.8064-0.11010.6274-33.43381.9223-9.8521
38.823-0.10260.685.45060.23225.3062-0.0860.8513-0.7311-0.91770.22950.46740.3889-0.3716-0.16270.9017-0.1825-0.00580.6924-0.08290.5329-43.7828-8.2705-4.1053
43.25741.1756-0.72553.7385-1.1951.552-0.2877-0.1444-0.07690.02780.2334-0.2231-0.3025-0.19790.04590.6196-0.03170.0010.5687-0.15410.4089-35.31372.29814.0132
57.8629-0.22333.84774.2379-3.63989.2949-0.3217-0.3532-0.0520.11570.3170.3715-0.2647-1.1689-0.36190.5892-0.00120.0420.5365-0.2010.514-49.2638-15.31078.6577
63.93931.0572-1.38533.1176-1.45017.7046-0.6408-0.36760.9371-0.17210.37070.0087-0.032-1.3185-0.06860.5715-0.09520.00030.7589-0.10930.7271-42.8953-0.810310.8567
74.3047-5.57983.2416.019-3.92044.6839-1.154-0.72512.43650.46560.3723-1.7704-0.34460.10451.05880.8146-0.0096-0.09950.6127-0.1011.025-33.97249.8236-35.7156
88.01750.9857-0.87195.2968-4.95524.71950.0745-0.07650.33410.3619-0.0678-0.9241-0.68690.08920.11450.50330.11840.00480.487-0.04980.6898-17.4038-16.9451-28.0269
99.3158-6.443.44435.0087-3.5354.2393-0.8428-0.9050.24181.46750.3526-0.6573-0.2827-0.26780.43230.62760.0113-0.08510.6965-0.08540.5965-33.5968-4.9532-22.0214
108.8449-2.63710.91734.9883-2.02643.146-0.4352-0.21010.45450.38640.1013-0.5403-0.0875-0.38570.27950.46150.0394-0.08650.4881-0.07060.4686-35.592-4.8324-30.2154
119.4945-1.6828-0.3589.1368-5.37363.4956-0.27850.9277-1.4142-2.29780.95920.96850.1984-0.5735-0.25040.81130.00510.00330.80320.06770.691-34.3172-13.2798-38.1842
124.9103-1.0538-0.45264.18370.32886.14840.08950.3153-0.07840.3094-0.04930.2012-0.0918-0.5296-0.01880.51280.0925-0.07860.5803-0.05690.5424-47.95275.0999-37.5176
135.90963.365-2.49183.2289-3.8027.2388-0.1851-0.3771-0.6304-0.17740.1412-0.41391.0959-0.9203-0.20030.9666-0.10150.00290.8886-0.02830.7248-42.533-1.1065-46.5537
143.68964.18-3.72895.2791-4.36863.8205-1.02851.2188-0.45220.0658-0.51510.97170.5893-0.52231.30261.1236-0.1332-0.1761.87050.1591.6304-43.56-14.1013-28.6891
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 312 )A265 - 312
2X-RAY DIFFRACTION2chain 'A' and (resid 313 through 335 )A313 - 335
3X-RAY DIFFRACTION3chain 'A' and (resid 336 through 368 )A336 - 368
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 435 )A369 - 435
5X-RAY DIFFRACTION5chain 'A' and (resid 436 through 456 )A436 - 456
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 478 )A457 - 478
7X-RAY DIFFRACTION7chain 'B' and (resid 265 through 297 )B265 - 297
8X-RAY DIFFRACTION8chain 'B' and (resid 298 through 312 )B298 - 312
9X-RAY DIFFRACTION9chain 'B' and (resid 313 through 337 )B313 - 337
10X-RAY DIFFRACTION10chain 'B' and (resid 338 through 393 )B338 - 393
11X-RAY DIFFRACTION11chain 'B' and (resid 394 through 408 )B394 - 408
12X-RAY DIFFRACTION12chain 'B' and (resid 409 through 456 )B409 - 456
13X-RAY DIFFRACTION13chain 'B' and (resid 457 through 472 )B457 - 472
14X-RAY DIFFRACTION14chain 'B' and (resid 473 through 481 )B473 - 481

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