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- PDB-7xv9: Crystal structure of the Human TR4 DNA-Binding Domain -

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Basic information

Entry
Database: PDB / ID: 7xv9
TitleCrystal structure of the Human TR4 DNA-Binding Domain
ComponentsNuclear receptor subfamily 2 group C member 2
KeywordsDNA BINDING PROTEIN / Nuclear receptor
Function / homology
Function and homology information


positive regulation of embryonic development / tumor necrosis factor-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of JNK cascade / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis ...positive regulation of embryonic development / tumor necrosis factor-mediated signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of JNK cascade / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / positive regulation of canonical NF-kappaB signal transduction / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm
Similarity search - Function
: / : / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / : / : / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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
Nuclear receptor subfamily 2 group C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 Å
AuthorsLiu, Y. / Chen, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structures of human TR4LBD-JAZF1 and TR4DBD-DNA complexes reveal the molecular basis of transcriptional regulation.
Authors: Liu, Y. / Ma, L. / Li, M. / Tian, Z. / Yang, M. / Wu, X. / Wang, X. / Shang, G. / Xie, M. / Chen, Y. / Liu, X. / Jiang, L. / Wu, W. / Xu, C. / Xia, L. / Li, G. / Dai, S. / Chen, Z.
History
DepositionMay 21, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 1, 2023Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Mar 8, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
A: Nuclear receptor subfamily 2 group C member 2
B: Nuclear receptor subfamily 2 group C member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6376
Polymers18,3762
Non-polymers2624
Water2,378132
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area910 Å2
ΔGint-8 kcal/mol
Surface area9520 Å2
Unit cell
Length a, b, c (Å)32.229, 32.229, 128.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Nuclear receptor subfamily 2 group C member 2 / Orphan nuclear receptor TAK1 / Orphan nuclear receptor TR4 / Testicular receptor 4


Mass: 9187.809 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR2C2, TAK1, TR4
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49116
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 1.81 Å3/Da / Density % sol: 32.02 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: Malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Aug 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.599→50 Å / Num. obs: 17222 / % possible obs: 99.6 % / Redundancy: 9.1 % / CC1/2: 0.9957 / Net I/σ(I): 21.2
Reflection shellResolution: 1.599→1.64 Å / Num. unique obs: 15147 / CC1/2: 0.933

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3DZU

3dzu


Resolution: 1.599→32.031 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.791 / SU ML: 0.062 / Cross valid method: FREE R-VALUE / ESU R: 0.109 / ESU R Free: 0.09
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1805 860 5.398 %
Rwork0.1764 15071 -
all0.177 --
obs-15931 92.515 %
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: 16.573 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å20 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.599→32.031 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1183 0 4 132 1319
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0131215
X-RAY DIFFRACTIONr_bond_other_d0.0010.0181112
X-RAY DIFFRACTIONr_angle_refined_deg1.7611.6381616
X-RAY DIFFRACTIONr_angle_other_deg1.5741.5862562
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7415164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.00621.03458
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.73115227
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.4231511
X-RAY DIFFRACTIONr_chiral_restr0.0910.2151
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021400
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02294
X-RAY DIFFRACTIONr_nbd_refined0.2310.2216
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.2971
X-RAY DIFFRACTIONr_nbtor_refined0.1710.2607
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0870.2564
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1720.273
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1970.224
X-RAY DIFFRACTIONr_nbd_other0.2310.282
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1280.219
X-RAY DIFFRACTIONr_mcbond_it1.6831.593642
X-RAY DIFFRACTIONr_mcbond_other1.6851.59641
X-RAY DIFFRACTIONr_mcangle_it2.4752.378800
X-RAY DIFFRACTIONr_mcangle_other2.4742.381801
X-RAY DIFFRACTIONr_scbond_it2.7151.911573
X-RAY DIFFRACTIONr_scbond_other2.7081.911573
X-RAY DIFFRACTIONr_scangle_it4.1922.734813
X-RAY DIFFRACTIONr_scangle_other4.1922.737814
X-RAY DIFFRACTIONr_lrange_it5.35219.0241354
X-RAY DIFFRACTIONr_lrange_other5.33218.7951336
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.599-1.640.104250.2602X-RAY DIFFRACTION49.0227
1.64-1.6850.253410.22755X-RAY DIFFRACTION63.3254
1.685-1.7340.275310.208999X-RAY DIFFRACTION88.0342
1.734-1.7870.232770.2081092X-RAY DIFFRACTION97.9062
1.787-1.8450.195620.1791049X-RAY DIFFRACTION99.7307
1.845-1.910.221580.1731050X-RAY DIFFRACTION99.8198
1.91-1.9820.216980.174955X-RAY DIFFRACTION100
1.982-2.0620.132430.166970X-RAY DIFFRACTION100
2.062-2.1540.209600.157918X-RAY DIFFRACTION99.8979
2.154-2.2580.16410.161873X-RAY DIFFRACTION100
2.258-2.380.194480.149837X-RAY DIFFRACTION100
2.38-2.5230.154460.158809X-RAY DIFFRACTION100
2.523-2.6960.147450.19752X-RAY DIFFRACTION100
2.696-2.910.229400.192686X-RAY DIFFRACTION100
2.91-3.1860.168420.182635X-RAY DIFFRACTION100
3.186-3.5570.192270.156598X-RAY DIFFRACTION100
3.557-4.0990.115300.16513X-RAY DIFFRACTION99.8162
4.099-50.147240.159424X-RAY DIFFRACTION100
5-6.9880.225160.198346X-RAY DIFFRACTION100
6.988-7.2290.1160.261208X-RAY DIFFRACTION98.1651

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