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- PDB-7xv8: Crystal structure of the Human TR4 DNA-Binding Domain Homodimer B... -

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Basic information

Entry
Database: PDB / ID: 7xv8
TitleCrystal structure of the Human TR4 DNA-Binding Domain Homodimer Bound to DR1 Response Element
Components
  • DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*CP*TP*GP*C)-3')
  • DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
  • Nuclear receptor subfamily 2 group C member 2
KeywordsDNA BINDING PROTEIN/DNA / Transcriptional regulation / DNA BINDING / PROTEIN-DNA COMPLEX / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


positive regulation of embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / cell differentiation ...positive regulation of embryonic development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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
DNA / DNA (> 10) / Nuclear receptor subfamily 2 group C member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
DNA molecule (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.199 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: Nuclear receptor subfamily 2 group C member 2
C: DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
D: DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*CP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,0188
Polymers28,7564
Non-polymers2624
Water1,06359
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: SAXS
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4110 Å2
ΔGint-31 kcal/mol
Surface area13260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.874, 51.874, 241.506
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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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: 8861.415 Da / Num. of mol.: 2
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: DNA chain DNA (5'-D(*GP*GP*CP*AP*GP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')


Mass: 5614.655 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*CP*TP*GP*C)-3')


Mass: 5418.502 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Chemical
ChemComp-ZN / ZINC ION


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


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.82 Å3/Da / Density % sol: 56.46 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / Details: PEG4000, sodium citrate, ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 3.199→50 Å / Num. obs: 5486 / % possible obs: 90.1 % / Redundancy: 5.8 % / CC1/2: 0.984 / Net I/σ(I): 9.2
Reflection shellResolution: 3.199→3.28 Å / Num. unique obs: 4919 / CC1/2: 0.95

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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: 3.199→47.708 Å / Cor.coef. Fo:Fc: 0.861 / Cor.coef. Fo:Fc free: 0.892 / WRfactor Rfree: 0.245 / WRfactor Rwork: 0.192 / SU B: 18.716 / SU ML: 0.325 / Average fsc free: 0.931 / Average fsc work: 0.9401 / Cross valid method: FREE R-VALUE / ESU R Free: 0.516
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2493 269 5.166 %
Rwork0.213 4938 -
all0.215 --
obs-5207 86.209 %
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: 53.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.038 Å20 Å20 Å2
2---0.038 Å20 Å2
3---0.075 Å2
Refinement stepCycle: LAST / Resolution: 3.199→47.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1024 726 0 59 1809
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0121846
X-RAY DIFFRACTIONr_bond_other_d0.0020.0191222
X-RAY DIFFRACTIONr_angle_refined_deg1.5481.4142635
X-RAY DIFFRACTIONr_angle_other_deg1.542.0552820
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9955151
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.51421.05338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.18215142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.609156
X-RAY DIFFRACTIONr_chiral_restr0.0720.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021687
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02431
X-RAY DIFFRACTIONr_nbd_refined0.20.2359
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2170.21199
X-RAY DIFFRACTIONr_nbtor_refined0.2040.2798
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0750.2686
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.246
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0280.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.210
X-RAY DIFFRACTIONr_nbd_other0.2940.221
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3020.22
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.130.21
X-RAY DIFFRACTIONr_mcbond_it4.7246.297608
X-RAY DIFFRACTIONr_mcbond_other4.7056.293607
X-RAY DIFFRACTIONr_mcangle_it7.2729.438757
X-RAY DIFFRACTIONr_mcangle_other7.2739.444758
X-RAY DIFFRACTIONr_scbond_it4.4926.1071238
X-RAY DIFFRACTIONr_scbond_other4.4826.1051237
X-RAY DIFFRACTIONr_scangle_it6.7869.1171878
X-RAY DIFFRACTIONr_scangle_other6.7869.1171878
X-RAY DIFFRACTIONr_lrange_it9.07265.2052259
X-RAY DIFFRACTIONr_lrange_other9.07465.1982258
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.199-3.2820.273170.226263X-RAY DIFFRACTION64.0732
3.282-3.3720.14780.205286X-RAY DIFFRACTION74.2424
3.372-3.4690.242160.193310X-RAY DIFFRACTION76.8868
3.469-3.5750.239120.204309X-RAY DIFFRACTION84.0314
3.575-3.6920.203180.206309X-RAY DIFFRACTION81.1414
3.692-3.8210.242200.181291X-RAY DIFFRACTION86.1496
3.821-3.9650.259150.189310X-RAY DIFFRACTION89.5317
3.965-4.1260.254190.156285X-RAY DIFFRACTION86.3636
4.126-4.3090.179150.154301X-RAY DIFFRACTION89.7727
4.309-4.5180.213200.176253X-RAY DIFFRACTION92.5424
4.518-4.7610.194150.172276X-RAY DIFFRACTION89.8148
4.761-5.0480.306130.178258X-RAY DIFFRACTION91.5541
5.048-5.3930.18100.196242X-RAY DIFFRACTION91.3044
5.393-5.8220.309140.222246X-RAY DIFFRACTION94.8905
5.822-6.3710.34120.209224X-RAY DIFFRACTION97.1193
6.371-7.1140.34590.225206X-RAY DIFFRACTION96.4126
7.114-8.1950.268160.212185X-RAY DIFFRACTION96.6346
7.195-8.9910.24570.19160X-RAY DIFFRACTION93.2961
7.991-9.940.14460.252135X-RAY DIFFRACTION94.6309
7.994-9.9760.41870.70489X-RAY DIFFRACTION93.2039

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