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- PDB-6j3n: RORgammat LBD complexed with Ursonic Acid and SRC2.2 -

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Basic information

Entry
Database: PDB / ID: 6j3n
TitleRORgammat LBD complexed with Ursonic Acid and SRC2.2
Components
  • LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
  • Nuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Inhibitor / nuclear 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
(5beta)-3-oxours-12-en-28-oic acid / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsLiu, Z.H. / Huang, J. / Tang, Y.
CitationJournal: To Be Published
Title: Structure of human RORgammat LBD with SCR2.2 at 1.99 Angstroms resolution
Authors: Liu, Z.H. / Huang, J. / Tang, Y.
History
DepositionJan 5, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 15, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 27, 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: LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1133
Polymers29,6582
Non-polymers4551
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area970 Å2
ΔGint-6 kcal/mol
Surface area12210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.930, 61.930, 155.870
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Nuclear receptor ROR-gamma / RAR-related orphan receptor gamma t / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 ...RAR-related orphan receptor gamma t / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 28635.154 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P51449
#2: Protein/peptide LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN / SRC2.2


Mass: 1023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-B8F / (5beta)-3-oxours-12-en-28-oic acid / Ursonic acid


Mass: 454.684 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H46O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.61 Å3/Da / Density % sol: 52.87 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 20% PEG3350 0.2M CaCl2

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Data collection

DiffractionMean temperature: 293 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979176 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Sep 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 1.99→48.486 Å / Num. obs: 21683 / % possible obs: 99.9 % / Redundancy: 24.8 % / Net I/σ(I): 19.6
Reflection shellResolution: 1.99→2.04 Å

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
CrysalisProdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→48.486 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 24.3
RfactorNum. reflection% reflection
Rfree0.2333 1066 4.93 %
Rwork0.1992 --
obs0.2008 21604 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 107.82 Å2 / Biso mean: 48.9704 Å2 / Biso min: 26.98 Å2
Refinement stepCycle: final / Resolution: 1.99→48.486 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1986 0 95 82 2163
Biso mean--71.94 50.7 -
Num. residues----246
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)
15.7859-3.26073.91717.0674-4.5083.9452-0.06210.00380.87920.105-0.2546-0.1543-0.7994-0.43370.32940.43180.06550.07570.35010.01120.431912.582915.8955-25.7324
22.6764-0.0024-0.18650.987-0.1811.0892-0.0917-0.20320.21910.3644-0.0504-0.3209-0.06070.30710.12920.40090.0042-0.05290.3916-0.00040.366426.8497-3.5079-9.9256
36.49471.3802-0.06183.15060.87043.1105-0.0985-0.1968-0.1373-0.1227-0.0240.32920.0752-0.37580.10250.3319-0.0137-0.04710.32430.06080.267810.8092-0.0144-20.6637
42.419-0.15070.29522.3769-1.0791.8717-0.0130.1158-0.12260.0915-0.1428-0.27060.15610.46980.13750.30650.0582-0.02260.35610.02820.274232.5767-6.8051-18.8117
52.38351.2676-1.39913.3495-1.09172.2274-0.02890.28940.0224-0.28320.12740.27960.1254-0.1524-0.0860.3605-0.0032-0.03330.30890.03120.328812.18245.3835-30.3484
61.00991.075-1.44293.2755-3.53465.4495-0.24290.0671-0.0929-0.72540.23690.0031.1039-0.3348-0.02550.4829-0.0368-0.05210.32540.01030.393917.9507-11.0031-19.6629
72.69411.00260.19449.1975-3.59697.2883-0.2784-0.497-1.57410.67680.06641.31090.1123-0.91310.19650.4451-0.03440.09930.72220.11070.67963.425-2.5156-10.144
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 264 through 284 )A264 - 284
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 337 )A285 - 337
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 368 )A338 - 368
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 410 )A369 - 410
5X-RAY DIFFRACTION5chain 'A' and (resid 411 through 456 )A411 - 456
6X-RAY DIFFRACTION6chain 'A' and (resid 457 through 509 )A457 - 509
7X-RAY DIFFRACTION7chain 'B' and (resid 688 through 695 )B688 - 695

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