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- PDB-4wlb: Crystal structure of RORc in complex with a partial inverse agoni... -

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Basic information

Entry
Database: PDB / ID: 4wlb
TitleCrystal structure of RORc in complex with a partial inverse agonist compound
Components
  • Nuclear receptor ROR-gamma
  • SRC-1 peptide
KeywordsTRANSCRIPTION / NUCLEAR RECEPTOR LIGAND BINDING DOMAIN
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 / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / 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 / T-helper cell differentiation / positive regulation of circadian rhythm / 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 / 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-3QQ / L(+)-TARTARIC ACID / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.702 Å
AuthorsBoenig, G. / Hymowitz, S.G. / Kiefer, J.R.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2014
Title: A reversed sulfonamide series of selective RORc inverse agonists.
Authors: van Niel, M.B. / Fauber, B.P. / Cartwright, M. / Gaines, S. / Killen, J.C. / Rene, O. / Ward, S.I. / de Leon Boenig, G. / Deng, Y. / Eidenschenk, C. / Everett, C. / Gancia, E. / Ganguli, A. ...Authors: van Niel, M.B. / Fauber, B.P. / Cartwright, M. / Gaines, S. / Killen, J.C. / Rene, O. / Ward, S.I. / de Leon Boenig, G. / Deng, Y. / Eidenschenk, C. / Everett, C. / Gancia, E. / Ganguli, A. / Gobbi, A. / Hawkins, J. / Johnson, A.R. / Kiefer, J.R. / La, H. / Lockey, P. / Norman, M. / Ouyang, W. / Qin, A. / Wakes, N. / Waszkowycz, B. / Wong, H.
History
DepositionOct 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 12, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 17, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_entity_src_syn / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_src_syn.pdbx_alt_source_flag / _pdbx_struct_oper_list.symmetry_operation / _software.classification
Revision 1.3Dec 27, 2023Group: 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: Nuclear receptor ROR-gamma
D: SRC-1 peptide
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8678
Polymers63,5694
Non-polymers1,2974
Water7,656425
1
A: Nuclear receptor ROR-gamma
D: SRC-1 peptide
hetero molecules

B: Nuclear receptor ROR-gamma
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,8678
Polymers63,5694
Non-polymers1,2974
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
Buried area3590 Å2
ΔGint-27 kcal/mol
Surface area23900 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-23 kcal/mol
Surface area22570 Å2
MethodPISA
3
A: Nuclear receptor ROR-gamma
D: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,5835
Polymers31,7852
Non-polymers7993
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint-8 kcal/mol
Surface area12480 Å2
MethodPISA
4
B: Nuclear receptor ROR-gamma
E: SRC-1 peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,2833
Polymers31,7852
Non-polymers4991
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-9 kcal/mol
Surface area12730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.787, 86.258, 91.854
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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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: 30853.502 Da / Num. of mol.: 2 / Fragment: ROR-gamma ligand binding domain
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 SRC-1 peptide


Mass: 931.172 Da / Num. of mol.: 2 / Fragment: SRC-1 peptide / Source method: obtained synthetically / Details: Synthetic peptide / Source: (synth.) Homo sapiens (human)
#3: Chemical ChemComp-3QQ / N-(4-fluorobenzyl)-N-(2-methylpropyl)-6-{[1-(methylsulfonyl)piperidin-4-yl]amino}pyridine-3-sulfonamide


Mass: 498.634 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H31FN4O4S2
#4: Chemical ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.23 Å3/Da / Density % sol: 44.74 %
Crystal growTemperature: 291 K / Method: vapor diffusion / Details: PEG 3350, Sodium formate

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Data collection

DiffractionMean temperature: 193 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.65→45 Å / Num. obs: 62573 / % possible obs: 97.4 % / Redundancy: 4 % / Biso Wilson estimate: 15.93 Å2 / Rmerge(I) obs: 0.085 / Rpim(I) all: 0.047 / Rrim(I) all: 0.097 / Χ2: 1.037 / Net I/av σ(I): 14.67 / Net I/σ(I): 8.2 / Num. measured all: 248553
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.65-1.682.40.76625920.3970.5660.9590.47682.3
1.68-1.712.60.71527550.4670.5030.8820.48887.2
1.71-1.742.80.66329230.5420.4480.8070.5692.4
1.74-1.783.10.61130920.6120.3930.7320.55396.8
1.78-1.823.70.55331460.720.3210.6430.59499.5
1.82-1.864.30.53231820.7590.2880.6060.59399.8
1.86-1.93.80.50431390.9250.2870.5820.75698.6
1.9-1.963.90.37931390.8150.2090.4351.598.7
1.96-2.014.40.28431660.9220.1520.3240.81499.7
2.01-2.084.20.26631540.9150.1440.3041.2999.5
2.08-2.154.30.1832160.9720.0970.2050.82199.7
2.15-2.244.10.14931190.9810.0810.170.95398.4
2.24-2.3440.15431270.960.0860.1771.59697.1
2.34-2.464.50.09632120.9930.050.1090.8899.9
2.46-2.624.40.0932080.9910.0480.1031.00399.8
2.62-2.824.50.07332040.9940.0390.0831.0299.6
2.82-3.114.50.05532470.9970.0290.0631.01999.9
3.11-3.554.50.05432390.9960.0280.0621.66399.3
3.55-4.484.30.04432680.9970.0230.051.82399.1
4.48-454.40.03334450.9980.0170.0371.14699.4

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.702→39.04 Å / FOM work R set: 0.8462 / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 22.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2263 5427 10.08 %
Rwork0.1777 48387 -
obs0.1825 53814 91.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 105.39 Å2 / Biso mean: 21.63 Å2 / Biso min: 3.24 Å2
Refinement stepCycle: final / Resolution: 1.702→39.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4148 0 86 425 4659
Biso mean--24.74 27.9 -
Num. residues----512
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074396
X-RAY DIFFRACTIONf_angle_d1.0345945
X-RAY DIFFRACTIONf_chiral_restr0.037652
X-RAY DIFFRACTIONf_plane_restr0.004752
X-RAY DIFFRACTIONf_dihedral_angle_d14.8041633
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7015-1.72090.3548690.256747254128
1.7209-1.74110.302720.233869176340
1.7411-1.76230.30851110.2263954106554
1.7623-1.78460.2631290.21541169129868
1.7846-1.80810.2661770.21631438161583
1.8081-1.83290.24961810.23361652183395
1.8329-1.85910.27692130.2541667188097
1.8591-1.88680.31421820.26381697187998
1.8868-1.91630.412020.34881654185694
1.9163-1.94770.37071660.2911684185096
1.9477-1.98130.28912320.20291674190699
1.9813-2.01730.23031960.183917641960100
2.0173-2.05610.23931940.193417261920100
2.0561-2.09810.26091860.20871781196799
2.0981-2.14370.22471800.17817471927100
2.1437-2.19360.21892000.171717511951100
2.1936-2.24840.27631860.21111710189697
2.2484-2.30920.29641700.19771688185896
2.3092-2.37720.17951990.149717721971100
2.3772-2.45390.21541990.144417421941100
2.4539-2.54160.21631790.156717871966100
2.5416-2.64330.21182000.158117711971100
2.6433-2.76360.22092020.166317371939100
2.7636-2.90920.21521970.164717911988100
2.9092-3.09140.21672130.172417581971100
3.0914-3.330.1952170.163217711988100
3.33-3.66490.18591840.15461789197399
3.6649-4.19470.18721730.13711836200999
4.1947-5.28280.14822000.13181800200099
5.2828-39.050.22732180.182119142132100
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)
12.02470.2257-0.11234.3470.2190.3823-0.05220.1120.381-0.50620.0953-0.4134-0.1479-0.0064-0.01950.1363-0.01270.03180.11870.02390.1271-13.137730.2731-20.4084
20.618-0.31220.3161.0145-0.09980.7969-0.02350.0039-0.0496-0.16810.0240.19360.1925-0.10720.00470.1098-0.0285-0.00080.1077-0.02650.0836-23.88562.619-12.2264
32.01240.27560.65571.6850.32910.9799-0.05870.1374-0.07590.02260.0393-0.316-0.01370.08860.05050.049-0.0155-0.01570.0750.0090.0884-10.283217.2138-9.8263
41.06860.01480.01561.36540.30950.9534-0.05460.0222-0.022-0.00820.00690.17980.1288-0.20780.04730.0888-0.03180.02210.1159-0.03180.0859-30.15367.3783-4.3917
52.034-0.37610.43281.4143-0.17220.6217-0.1095-0.01130.2860.08050.0251-0.1479-0.0419-0.01740.06580.0895-0.0063-0.03640.0730.01420.1019-14.317127.6877-9.7864
61.7062-1.11331.3512.9251-1.92814.0707-0.1013-0.22430.24290.31980.17490.28130.0662-0.19290.06120.09530.0125-0.02340.1160.02140.1921-26.679929.4416-6.3582
70.2785-0.5215-0.15482.0630.40311.0538-0.1128-0.01010.07780.55640.1447-0.6360.36250.03070.06550.19190.041-0.05890.13610.0162-0.0233-12.45482.44490.8923
81.2527-0.75940.44364.7332-0.41321.03190.1716-0.0813-0.23580.6789-0.01810.0930.17940.0382-0.24370.2266-0.0101-0.03670.10320.0260.1159-18.5609-36.7651-4.9148
91.06050.04390.75011.9558-0.49880.8682-0.17520.04970.03350.08370.33470.6323-0.0425-0.3133-0.06390.10950.01140.04450.17870.0610.2547-28.5601-7.7739-20.9207
100.89360.44370.26763.215-1.08421.10120.0071-0.05350.04690.3070.0057-0.0536-0.0523-0.0739-0.06820.1008-0.0091-0.010.0938-0.01630.0514-14.5526-10.5586-13.6
112.3350.3767-0.04271.5235-0.03220.59870.09820.1038-0.75610.3193-0.1023-0.59630.11280.1371-0.12350.1341-0.0002-0.13470.02230.09930.2889-9.8059-24.0624-11.2264
121.31480.3990.38411.7116-0.17760.2556-0.06420.17330.0329-0.35930.13510.24320.01420.0108-0.04940.1397-0.0169-0.03240.1260.00960.091-22.2991-13.9276-27.6464
133.29650.74590.12732.3048-0.02151.1918-0.21370.0146-0.2818-0.28090.2439-0.89250.00680.1392-0.2514-0.1155-0.0189-0.07160.08870.00390.3293-12.7441-30.2357-14.9412
141.8603-0.18520.6521.6421-0.2131.5261-0.0603-0.1019-0.04680.0849-0.0124-0.78820.26910.055-0.35270.09870.012-0.06810.06510.03090.3652-13.2326-39.3696-12.1073
153.01872.2504-1.29533.1123-1.05052.13540.32260.1534-0.2381-0.41460.0287-0.3473-0.16540.13730.07190.1879-0.0080.04140.1095-0.01420.1707-19.8279-36.1496-24.2931
160.5645-0.2849-0.29751.7555-0.0111.4037-0.09250.0667-0.0914-0.090.1649-0.591-0.06990.202-0.02750.0934-0.03450.04660.1649-0.02260.1208-5.052-9.1493-21.2433
173.4258-1.09592.03244.47080.31982.88160.32570.12480.366-0.2382-0.1304-0.6216-0.10590.18790.01140.1852-0.02350.05810.1722-0.04310.2542-0.09799.4259-12.911
183.864-0.1081-1.00284.5281-0.96483.47460.169-0.3174-0.02550.4586-0.0048-0.64970.41540.09450.07580.3648-0.0226-0.13750.23190.00820.2088-3.7953-16.1074-2.8942
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 239 through 263 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 264 through 316 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 317 through 347 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 348 through 389 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 390 through 435 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 436 through 449 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 450 through 486 )A0
8X-RAY DIFFRACTION8chain 'B' and (resid 239 through 263 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 264 through 291 )B0
10X-RAY DIFFRACTION10chain 'B' and (resid 292 through 316 )B0
11X-RAY DIFFRACTION11chain 'B' and (resid 317 through 347 )B0
12X-RAY DIFFRACTION12chain 'B' and (resid 348 through 389 )B0
13X-RAY DIFFRACTION13chain 'B' and (resid 390 through 414 )B0
14X-RAY DIFFRACTION14chain 'B' and (resid 415 through 435 )B0
15X-RAY DIFFRACTION15chain 'B' and (resid 436 through 449 )B0
16X-RAY DIFFRACTION16chain 'B' and (resid 450 through 486 )B0
17X-RAY DIFFRACTION17chain 'D' and (resid 8 through 15 )D0
18X-RAY DIFFRACTION18chain 'E' and (resid 8 through 15 )E0

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