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- PDB-7xva: Crystal structure of the Human TR4 Ligand Binding Domain in compl... -

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Basic information

Entry
Database: PDB / ID: 7xva
TitleCrystal structure of the Human TR4 Ligand Binding Domain in complex with the JAZF1 corepressor fragment
Components
  • Juxtaposed with another zinc finger protein 1
  • Nuclear receptor subfamily 2 group C member 2
KeywordsTRANSCRIPTION / Nuclear receptor / Corepressor / Transcriptional regulation
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 / fibrillar center / nuclear receptor activity / sequence-specific double-stranded DNA binding / nervous system development / DNA-binding transcription activator activity, RNA polymerase II-specific ...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 / fibrillar center / 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 / metal ion binding / cytosol
Similarity search - Function
: / : / : / : / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Retinoid X Receptor / Retinoid X Receptor / Zinc finger C2H2-type / Nuclear hormone receptor ...: / : / : / : / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Retinoid X Receptor / Retinoid X Receptor / Zinc finger C2H2-type / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
JAZF zinc finger 1 / Nuclear receptor subfamily 2 group C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.856 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

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Assembly

Deposited unit
A: Nuclear receptor subfamily 2 group C member 2
B: Juxtaposed with another zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)31,8912
Polymers31,8912
Non-polymers00
Water2,144119
1
A: Nuclear receptor subfamily 2 group C member 2
B: Juxtaposed with another zinc finger protein 1

A: Nuclear receptor subfamily 2 group C member 2
B: Juxtaposed with another zinc finger protein 1


Theoretical massNumber of molelcules
Total (without water)63,7834
Polymers63,7834
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_655-x+1,y,-z1
Buried area6160 Å2
ΔGint-47 kcal/mol
Surface area21900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.851, 76.851, 98.365
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322

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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: 28913.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR2C2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P49116
#2: Protein/peptide Juxtaposed with another zinc finger protein 1


Mass: 2978.276 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: JAZF1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: C9JGY8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: HEPES, ammonium sulfate, sodium acetate, MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 7, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.856→50 Å / Num. obs: 25132 / % possible obs: 98 % / Redundancy: 9.5 % / CC1/2: 0.998 / Net I/σ(I): 36
Reflection shellResolution: 1.856→1.9 Å / Num. unique obs: 22758 / CC1/2: 0.996

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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: 3P0U

3p0u


Resolution: 1.856→28.09 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / WRfactor Rfree: 0.213 / WRfactor Rwork: 0.191 / SU B: 2.955 / SU ML: 0.086 / Average fsc free: 0.9264 / Average fsc work: 0.9315 / Cross valid method: FREE R-VALUE / ESU R: 0.14 / ESU R Free: 0.125
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2187 1248 5.2 %
Rwork0.1965 22753 -
all0.198 --
obs-24001 93.747 %
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: 19.405 Å2
Baniso -1Baniso -2Baniso -3
1--0.002 Å20 Å2-0 Å2
2---0.002 Å2-0 Å2
3---0.005 Å2
Refinement stepCycle: LAST / Resolution: 1.856→28.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1886 0 0 119 2005
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0131923
X-RAY DIFFRACTIONr_bond_other_d0.0010.0171776
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.6382600
X-RAY DIFFRACTIONr_angle_other_deg1.4291.5664077
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9475245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.43422.82485
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.11715313
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.073159
X-RAY DIFFRACTIONr_chiral_restr0.0820.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022158
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02438
X-RAY DIFFRACTIONr_nbd_refined0.2070.2427
X-RAY DIFFRACTIONr_symmetry_nbd_other0.180.21516
X-RAY DIFFRACTIONr_nbtor_refined0.1680.2968
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.2849
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1320.280
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3560.212
X-RAY DIFFRACTIONr_nbd_other0.2420.250
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2190.28
X-RAY DIFFRACTIONr_mcbond_it2.0352.057981
X-RAY DIFFRACTIONr_mcbond_other2.0342.058981
X-RAY DIFFRACTIONr_mcangle_it3.1843.0381214
X-RAY DIFFRACTIONr_mcangle_other3.1833.0411215
X-RAY DIFFRACTIONr_scbond_it2.7242.138941
X-RAY DIFFRACTIONr_scbond_other2.7212.138941
X-RAY DIFFRACTIONr_scangle_it4.2043.1141386
X-RAY DIFFRACTIONr_scangle_other4.2033.1161387
X-RAY DIFFRACTIONr_lrange_it5.79923.4972223
X-RAY DIFFRACTIONr_lrange_other5.66223.3582207
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.856-1.9040.339490.32894X-RAY DIFFRACTION50.8082
1.904-1.9560.283600.2871478X-RAY DIFFRACTION85.3496
1.956-2.0130.254710.261602X-RAY DIFFRACTION94.5198
2.013-2.0750.288910.2221570X-RAY DIFFRACTION97.4194
2.075-2.1430.243960.211531X-RAY DIFFRACTION98.2488
2.143-2.2180.238810.1941507X-RAY DIFFRACTION98.6948
2.218-2.3020.208830.21445X-RAY DIFFRACTION98.4536
2.302-2.3960.214690.181417X-RAY DIFFRACTION98.6065
2.396-2.5020.202800.1781353X-RAY DIFFRACTION99.101
2.502-2.6240.246780.1821273X-RAY DIFFRACTION98.9019
2.624-2.7660.215590.1771263X-RAY DIFFRACTION98.9521
2.766-2.9330.179590.181175X-RAY DIFFRACTION99.1961
2.933-3.1360.2530.1731124X-RAY DIFFRACTION99.2411
3.136-3.3860.225690.1771028X-RAY DIFFRACTION99.3659
3.386-3.7090.196630.18956X-RAY DIFFRACTION99.4146
3.709-4.1450.187570.168879X-RAY DIFFRACTION99.4687
4.145-4.7840.186480.163786X-RAY DIFFRACTION99.7608
4.784-5.8540.251440.225664X-RAY DIFFRACTION98.1969
5.854-8.2550.23200.255505X-RAY DIFFRACTION90.5172
7.255-9.8510.192180.219303X-RAY DIFFRACTION89.415

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