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- PDB-7e3m: RORgamma LBD complexed with Panaxatriol and SRC2.2 -

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Basic information

Entry
Database: PDB / ID: 7e3m
TitleRORgamma LBD complexed with Panaxatriol and SRC2.2
Components
  • LYS-ILE-LEU-HIS-ARG-LEU-LEU-GLN
  • Nuclear receptor ROR-gamma
KeywordsIMMUNE SYSTEM/INHIBITOR / nuclear receptor / IMMUNE SYSTEM - inhibitor complex / IMMUNE SYSTEM-INHIBITOR complex
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 / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
Similarity search - Domain/homology
Chem-HVL / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.8 Å
AuthorsLiu, Z.H. / Huang, J. / Lu, W.Q. / Tang, Y. / Wu, Z.R.
CitationJournal: To Be Published
Title: Structure of human RORgammat LBD with SRC2.2 at 2.80 Angstroms resolution
Authors: Liu, Z.H. / Huang, J. / Wu, Z.R. / Tang, Y. / Lu, W.Q.
History
DepositionFeb 9, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 23, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)29,8083
Polymers29,3312
Non-polymers4771
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area960 Å2
ΔGint-7 kcal/mol
Surface area12240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.446, 62.446, 159.766
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 / 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: 28307.824 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


Mass: 1023.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Chemical ChemComp-HVL / (3R,5R,6S,8R,9R,10R,12R,13R,14R,17S)-4,4,8,10,14-pentamethyl-17-[(2R)-2,6,6-trimethyloxan-2-yl]-2,3,5,6,7,9,11,12,13,15,16,17-dodecahydro-1H-cyclopenta[a]phenanthrene-3,6,12-triol


Mass: 476.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H52O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 18 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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 %
Description: THE ENTRY CONTAINS FRIEDEL PAIRS IN I/F_PLUS/MINUS COLUMNS.
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: Dec 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979176 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 8384 / % possible obs: 100 % / Redundancy: 20 % / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.013 / Rrim(I) all: 0.067 / Χ2: 0.943 / Net I/σ(I): 10.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.81-2.86260.3074190.9960.0610.3130.951100
2.86-2.9125.90.243900.9920.0480.2450.975100
2.91-2.9725.50.2154050.9950.0430.2190.978100
2.97-3.0325.60.1973920.9950.0390.20.983100
3.03-3.0925.50.1774060.9920.0360.1810.981100
3.09-3.1623.60.1474230.9950.0310.150.96100
3.16-3.2421.70.1193890.9970.0260.1220.99799.7
3.24-3.3324.70.114210.9980.0220.1121.012100
3.33-3.4326.80.0994070.9980.0190.1011.011100
3.43-3.5426.50.0814110.9980.0160.0830.986100
3.54-3.6726.10.0744140.9990.0150.0751.012100
3.67-3.8125.60.0644070.9990.0130.0650.976100
3.81-3.9925.60.0564180.9990.0110.0570.991100
3.99-4.225.10.0494250.9990.010.050.979100
4.2-4.4624.10.04641510.010.0470.954100
4.46-4.820.90.0414230.9990.0090.0420.93100
4.8-5.2924.90.0424240.9990.0080.0420.881100
5.29-6.0524.90.0434380.9990.0090.0440.832100
6.05-7.62230.0384510.9990.0080.0390.752100
7.62-5018.70.0315060.9990.0070.0310.70499.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4XT9
Resolution: 2.8→39.94 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.712 / SU ML: 0.261 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.393 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2693 385 4.6 %RANDOM
Rwork0.1942 ---
obs0.1974 7916 99.48 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 89.27 Å2 / Biso mean: 34.691 Å2 / Biso min: 16.56 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: final / Resolution: 2.8→39.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2025 0 34 18 2077
Biso mean--39.8 32.43 -
Num. residues----251
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0192106
X-RAY DIFFRACTIONr_bond_other_d0.0010.022061
X-RAY DIFFRACTIONr_angle_refined_deg1.471.9762854
X-RAY DIFFRACTIONr_angle_other_deg0.78934718
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9945249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.60623.09397
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.09815377
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.591515
X-RAY DIFFRACTIONr_chiral_restr0.0790.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022305
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02510
LS refinement shellResolution: 2.802→2.874 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 25 -
Rwork0.213 552 -
all-577 -
obs--98.63 %

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