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- PDB-8wuy: Crystal Structure of TR3 LBD in complex with para-positioned 3,4,... -

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Basic information

Entry
Database: PDB / ID: 8wuy
TitleCrystal Structure of TR3 LBD in complex with para-positioned 3,4,5-trisubstituted benzene derivatives
ComponentsNuclear receptor subfamily 4immunitygroup A member 1
KeywordsTRANSCRIPTION / Complex
Function / homology
Function and homology information


neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis ...neurotransmitter secretion involved in regulation of skeletal muscle contraction / regulation of type B pancreatic cell proliferation / non-canonical inflammasome complex assembly / detection of lipopolysaccharide / cellular response to corticotropin-releasing hormone stimulus / AKT phosphorylates targets in the nucleus / endothelial cell chemotaxis / nuclear glucocorticoid receptor binding / cellular response to fibroblast growth factor stimulus / cell migration involved in sprouting angiogenesis / fat cell differentiation / skeletal muscle cell differentiation / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of cell cycle / cellular response to vascular endothelial growth factor stimulus / response to electrical stimulus / positive regulation of endothelial cell proliferation / response to amphetamine / lipopolysaccharide binding / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / presynapse / DNA-binding transcription activator activity, RNA polymerase II-specific / nuclear membrane / transcription regulator complex / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / inflammatory response / positive regulation of apoptotic process / protein heterodimerization activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / apoptotic process / chromatin / regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / mitochondrion / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / cytosol
Similarity search - Function
Orphan nuclear receptor, HMR type / Orphan nuclear 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 ...Orphan nuclear receptor, HMR type / Orphan nuclear 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
Similarity search - Domain/homology
Chem-XBF / Nuclear receptor subfamily 4immunitygroup A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsHong, W.B. / Chen, X.Q. / Lin, T.W.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Bioorg.Chem. / Year: 2024
Title: Structure-based design and synthesis of anti-fibrotic compounds derived from para-positioned 3,4,5-trisubstituted benzene.
Authors: Hong, W. / Xiao, T. / Lin, G. / Liu, C. / Li, H. / Li, Y. / Hu, H. / Wu, S. / Wang, S. / Liang, Z. / Lin, T. / Liu, J. / Chen, X.
History
DepositionOct 21, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 24, 2024Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 4immunitygroup A member 1
B: Nuclear receptor subfamily 4immunitygroup A member 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3813
Polymers55,0862
Non-polymers2951
Water1,33374
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1160 Å2
ΔGint-14 kcal/mol
Surface area21750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.844, 76.441, 129.417
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nuclear receptor subfamily 4immunitygroup A member 1


Mass: 27542.963 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR4A1 / Production host: Escherichia coli (E. coli) / References: UniProt: P22736
#2: Chemical ChemComp-XBF / ~{N}-methyl-~{N}-octyl-3,4,5-tris(oxidanyl)benzamide


Mass: 295.374 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H25NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 74 / 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: 3.36 Å3/Da / Density % sol: 63.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: PEG4000, Sodium citrate, Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 23602 / % possible obs: 99.9 % / Redundancy: 6.3 % / CC1/2: 0.889 / Net I/σ(I): 19.769
Reflection shellResolution: 2.6→2.64 Å / Num. unique obs: 23602 / CC1/2: 0.883

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→33.633 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.901 / SU B: 8.984 / SU ML: 0.193 / Cross valid method: FREE R-VALUE / ESU R: 0.371 / ESU R Free: 0.261
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2426 1168 4.949 %
Rwork0.2006 22434 -
all0.203 --
obs-23602 99.624 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 39.022 Å2
Baniso -1Baniso -2Baniso -3
1-0.194 Å20 Å20 Å2
2--0.054 Å2-0 Å2
3----0.248 Å2
Refinement stepCycle: LAST / Resolution: 2.6→33.633 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3584 0 21 74 3679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0133722
X-RAY DIFFRACTIONr_bond_other_d0.0010.0153670
X-RAY DIFFRACTIONr_angle_refined_deg1.5631.6335045
X-RAY DIFFRACTIONr_angle_other_deg1.2441.5738466
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1265464
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27721.111189
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.46315657
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2861529
X-RAY DIFFRACTIONr_chiral_restr0.0720.2472
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024105
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02825
X-RAY DIFFRACTIONr_nbd_refined0.2130.2808
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1750.23189
X-RAY DIFFRACTIONr_nbtor_refined0.1640.21801
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21903
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1640.277
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1850.212
X-RAY DIFFRACTIONr_nbd_other0.1910.256
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1840.25
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.120.21
X-RAY DIFFRACTIONr_mcbond_it3.173.9451835
X-RAY DIFFRACTIONr_mcbond_other3.1653.9441834
X-RAY DIFFRACTIONr_mcangle_it4.8765.8952288
X-RAY DIFFRACTIONr_mcangle_other4.8765.8972289
X-RAY DIFFRACTIONr_scbond_it3.7064.2721887
X-RAY DIFFRACTIONr_scbond_other3.7054.2731888
X-RAY DIFFRACTIONr_scangle_it5.9246.2562751
X-RAY DIFFRACTIONr_scangle_other5.9226.2572752
X-RAY DIFFRACTIONr_lrange_it9.29272.51515002
X-RAY DIFFRACTIONr_lrange_other9.29472.52114984
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.660.302930.2421585X-RAY DIFFRACTION97.0503
2.66-2.7330.323920.2191553X-RAY DIFFRACTION99.697
2.733-2.8120.285640.2121582X-RAY DIFFRACTION100
2.812-2.8980.27880.2121494X-RAY DIFFRACTION100
2.898-2.9930.3680.2191477X-RAY DIFFRACTION100
2.993-3.0980.312850.2361397X-RAY DIFFRACTION100
3.098-3.2150.252710.2231372X-RAY DIFFRACTION100
3.215-3.3460.3610.2211333X-RAY DIFFRACTION100
3.346-3.4940.275720.2071265X-RAY DIFFRACTION100
3.494-3.6640.218490.1951233X-RAY DIFFRACTION100
3.664-3.8620.247560.1851157X-RAY DIFFRACTION100
3.862-4.0950.197630.1811102X-RAY DIFFRACTION99.9142
4.095-4.3770.203520.1681035X-RAY DIFFRACTION100
4.377-4.7260.18510.15974X-RAY DIFFRACTION100
4.726-5.1740.195510.171899X-RAY DIFFRACTION100
5.174-5.780.233460.205821X-RAY DIFFRACTION100
5.78-6.6660.195300.195732X-RAY DIFFRACTION100
6.666-8.1430.238390.218625X-RAY DIFFRACTION99.6997
8.143-100.197220.161504X-RAY DIFFRACTION99.6212

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