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- PDB-5k3m: Crystal structure of Retinoic acid receptor-related orphan recept... -

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Basic information

Entry
Database: PDB / ID: 5k3m
TitleCrystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with UUA
ComponentsNuclear receptor ROR-gamma
KeywordsPROTEIN BINDING / double helix
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
Ursolic acid / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.894 Å
Model detailsROR gamma ligand binding domain complex with 444
AuthorsHuang, P. / Rastinejad, F.
CitationJournal: To be published
Title: Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand binding domain complex with UUA
Authors: Lu, J. / Rastinejad, F.
History
DepositionMay 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2017Provider: repository / Type: Initial release
Revision 1.1Mar 6, 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

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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)58,3564
Polymers57,4432
Non-polymers9132
Water0
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1782
Polymers28,7211
Non-polymers4571
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1782
Polymers28,7211
Non-polymers4571
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)89.702, 89.702, 153.793
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: 28721.289 Da / Num. of mol.: 2 / Fragment: ligand binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Plasmid: pET28 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL / References: UniProt: P51449
#2: Chemical ChemComp-6Q5 / Ursolic acid / (3beta,5beta,18alpha,20beta)-3-hydroxyurs-12-en-28-oic acid / Ursolic acid


Mass: 456.700 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C30H48O3

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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: 3.11 Å3/Da / Density % sol: 64.35 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: 0.4M Potassium sodium tartrate tetrahydrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
Reflection twinOperator: h,-h-k,-l / Fraction: 0.11
ReflectionResolution: 2.9→50 Å / Num. obs: 15621 / % possible obs: 99.7 % / Redundancy: 5.4 % / Rmerge(I) obs: 0.101 / Χ2: 1.39 / Net I/av σ(I): 20.13 / Net I/σ(I): 10.4 / Num. measured all: 84240
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.9-2.953.80.7187440.93998.8
2.95-34.30.7817930.9599.6
3-3.065.40.7967590.999100
3.06-3.125.60.6268030.963100
3.12-3.195.60.4427821.059100
3.19-3.275.60.4667701.047100
3.27-3.355.60.3087911.084100
3.35-3.445.60.2437751.089100
3.44-3.545.60.2527821.173100
3.54-3.655.60.2277721.59100
3.65-3.785.50.1777942.506100
3.78-3.945.60.1187841.361100
3.94-4.115.60.1057811.57299.9
4.11-4.335.60.0937761.437100
4.33-4.65.60.0797751.425100
4.6-4.965.60.0748001.506100
4.96-5.465.60.0787821.556100
5.46-6.245.50.0847881.765100
6.24-7.865.30.0747921.631100
7.86-505.10.0787781.91995.1

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
HKL-2000data collection
PDB_EXTRACT3.2data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.894→34.67 Å / FOM work R set: 0.645 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 40.91 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.295 764 5.17 %
Rwork0.2654 13994 -
obs0.2675 14791 94.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 281.64 Å2 / Biso mean: 129.25 Å2 / Biso min: 68.76 Å2
Refinement stepCycle: final / Resolution: 2.894→34.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3626 0 66 0 3692
Biso mean--137.22 --
Num. residues----444
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053770
X-RAY DIFFRACTIONf_angle_d0.9035096
X-RAY DIFFRACTIONf_chiral_restr0.064568
X-RAY DIFFRACTIONf_plane_restr0.002638
X-RAY DIFFRACTIONf_dihedral_angle_d16.8611444
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8971-3.12060.3641430.37662624276785
3.1206-3.43430.39891570.39382762291989
3.4343-3.93040.36531510.35072761291289
3.9304-4.94860.32841530.27842903305693
4.9486-30.96090.23381600.19592944310494
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)
12.47090.2585-7.92546.75563.26613.5364-1.70470.0181-1.84180.9515-0.48080.29570.47460.33741.97531.3803-0.1168-0.17670.84790.21811.1312-37.068421.716915.1437
23.0309-0.52871.82912.83681.0324-0.6875-0.5779-0.1222-1.0944-0.93140.16980.10120.26580.25820.37351.61720.31060.01851.0788-0.1131.0004-5.975117.50025.9206
35.3694-0.5747-0.52723.01981.69260.45960.29810.5925-1.3077-0.117-0.4471-0.33090.48330.971-0.03631.95960.2173-0.27331.3859-0.01330.6911-17.727526.7752-2.1565
47.8731-2.07253.15082.63312.12635.29191.4709-1.79851.18130.5885-1.9412.57620.5793-1.52650.6461.3488-0.3240.11812.1953-0.78311.2877-39.848532.23521.4181
54.6179-2.39012.98515.29131.57874.87150.40320.4407-0.3068-0.29430.1645-0.50710.39150.5652-0.61840.9967-0.30560.08941.2361-0.06090.778-15.978127.32257.6157
60.8701-0.5247-2.45161.435-2.15467.57630.10970.22470.5545-0.03450.2114-0.63141.27481.8547-0.7310.83310.0661-0.2111.5420.00071.3778-6.360332.40469.2785
76.32163.06732.20012.10741.13084.020.0375-0.19860.13260.0765-0.10630.2107-0.43120.3220.09170.8534-0.12160.0620.9436-0.06350.8655-31.034532.908616.6834
84.1371-0.7128-3.94291.6339-0.13082.37840.6175-0.50630.1244-0.1153-0.60870.4001-0.6734-0.15440.06880.8585-0.2184-0.28531.17830.08611.2436-15.47439.73182.8988
94.4201-3.76356.83475.1792-4.38348.0821-0.3529-0.13421.6738-0.3846-0.2249-0.5109-0.72280.80060.53951.3101-0.52890.29220.9365-0.15341.4336-34.974420.5728-14.274
102.0023-6.2019-3.95919.44492.67188.7891-0.47171.62210.1720.34210.4665-0.60210.22830.76180.0471.1025-0.2701-0.20391.4420.0021.0323-18.56685.2422-10.2803
118.87584.8431-4.15612.7902-3.05342.5091-0.32870.1442-0.17341.53940.646-0.6435-1.24970.0988-0.44151.19770.1733-0.06191.4189-0.14910.9777-16.9777-13.7624-1.6882
126.8679-1.03630.46352.68240.14176.0556-0.1235-0.7582-0.2131.7763-1.0859-0.34920.42981.44570.98841.2215-0.10970.23621.43030.02460.7341-30.4220.4473.4066
135.9979-2.5019-1.03927.10074.59762.331-0.4351-0.19780.3113-0.01420.01580.2891-0.3905-0.08890.42831.7001-0.1477-0.22850.84480.06490.6029-40.1529.893-3.076
147.4914-4.67740.33354.6665-5.03045.1510.51150.8693-0.27170.3514-0.21550.3791-0.3551.031-0.35181.26380.0284-0.01161.008-0.18990.8165-27.3616-8.7923-9.7067
156.1425-0.0738-1.85270.3415-1.64958.67540.36650.0995-0.4324-0.2788-0.42270.3852-0.2797-0.59790.02481.2883-0.03-0.09090.4736-0.10390.8565-43.742112.2025-13.4957
162.7535-2.7077-0.52516.6254-2.93238.4691-0.08410.6603-1.3833-0.3048-0.23340.5878-0.54390.28190.3280.959-0.2089-0.07750.8734-0.22441.053-40.7666-2.6043-10.2675
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 284 )A265 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 312 )A285 - 312
3X-RAY DIFFRACTION3chain 'A' and (resid 313 through 337 )A313 - 337
4X-RAY DIFFRACTION4chain 'A' and (resid 338 through 347 )A338 - 347
5X-RAY DIFFRACTION5chain 'A' and (resid 348 through 385 )A348 - 385
6X-RAY DIFFRACTION6chain 'A' and (resid 386 through 408 )A386 - 408
7X-RAY DIFFRACTION7chain 'A' and (resid 409 through 468 )A409 - 468
8X-RAY DIFFRACTION8chain 'A' and (resid 469 through 486 )A469 - 486
9X-RAY DIFFRACTION9chain 'B' and (resid 265 through 284 )B265 - 284
10X-RAY DIFFRACTION10chain 'B' and (resid 285 through 296 )B285 - 296
11X-RAY DIFFRACTION11chain 'B' and (resid 297 through 312 )B297 - 312
12X-RAY DIFFRACTION12chain 'B' and (resid 313 through 336 )B313 - 336
13X-RAY DIFFRACTION13chain 'B' and (resid 337 through 368 )B337 - 368
14X-RAY DIFFRACTION14chain 'B' and (resid 369 through 410 )B369 - 410
15X-RAY DIFFRACTION15chain 'B' and (resid 411 through 457 )B411 - 457
16X-RAY DIFFRACTION16chain 'B' and (resid 458 through 486 )B458 - 486

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