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- PDB-8j0q: Structure of DNA binding domain of human TFAP2B -

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Basic information

Entry
Database: PDB / ID: 8j0q
TitleStructure of DNA binding domain of human TFAP2B
ComponentsTranscription factor AP-2-beta
KeywordsDNA BINDING PROTEIN / TFAP2 family
Function / homology
Function and homology information


metanephric nephron development / ductus arteriosus closure / forelimb morphogenesis / distal tubule development / collecting duct development / hindlimb morphogenesis / aorta morphogenesis / Specification of the neural plate border / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / retina layer formation ...metanephric nephron development / ductus arteriosus closure / forelimb morphogenesis / distal tubule development / collecting duct development / hindlimb morphogenesis / aorta morphogenesis / Specification of the neural plate border / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / retina layer formation / regulation of BMP signaling pathway / smooth muscle tissue development / sympathetic nervous system development / Activation of the TFAP2 (AP-2) family of transcription factors / skin development / fat cell differentiation / regulation of cell differentiation / SUMOylation of transcription factors / cis-regulatory region sequence-specific DNA binding / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / regulation of insulin secretion / RNA polymerase II transcription regulatory region sequence-specific DNA binding / kidney development / glucose metabolic process / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / neuron apoptotic process / sequence-specific DNA binding / negative regulation of neuron apoptotic process / transcription by RNA polymerase II / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / response to xenobiotic stimulus / DNA-binding transcription factor activity / protein heterodimerization activity / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / positive regulation of cell population proliferation / chromatin binding / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus
Similarity search - Function
Transcription factor AP-2 beta / Transcription factor AP-2 / Transcription factor AP-2, C-terminal / Transcription factor AP-2
Similarity search - Domain/homology
Transcription factor AP-2-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsLiu, K. / Xiao, Y.Q. / Li, W.F. / Min, J.R.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31770834 China
CitationJournal: Nucleic Acids Res. / Year: 2023
Title: Structural basis for specific DNA sequence motif recognition by the TFAP2 transcription factors.
Authors: Liu, K. / Xiao, Y. / Gan, L. / Li, W. / Zhang, J. / Min, J.
History
DepositionApr 11, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 5, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 6, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Transcription factor AP-2-beta
B: Transcription factor AP-2-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1604
Polymers51,9752
Non-polymers1842
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6060 Å2
ΔGint-64 kcal/mol
Surface area18690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.212, 81.829, 115.628
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Transcription factor AP-2-beta / AP2-beta / Activating enhancer-binding protein 2-beta


Mass: 25987.732 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAP2B / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q92481
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.33 Å3/Da / Density % sol: 47.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium citrate tribasic dihydrate and 20% PEG 3350 (w/v)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.4→43.41 Å / Num. obs: 19146 / % possible obs: 97.2 % / Redundancy: 6.5 % / CC1/2: 0.995 / Net I/σ(I): 12.9
Reflection shellResolution: 2.4→2.49 Å / Num. unique obs: 2025 / CC1/2: 0.97

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→38.36 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.507 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.245 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24112 978 5.1 %RANDOM
Rwork0.18385 ---
obs0.18681 18118 97.12 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 45.962 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.4→38.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3005 0 12 57 3074
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0133059
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172957
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.6434124
X-RAY DIFFRACTIONr_angle_other_deg1.3131.5726859
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5455384
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.05321.141149
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.78615545
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6811525
X-RAY DIFFRACTIONr_chiral_restr0.0770.2403
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023348
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02611
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.9024.6621560
X-RAY DIFFRACTIONr_mcbond_other3.9014.6611559
X-RAY DIFFRACTIONr_mcangle_it5.76.9471936
X-RAY DIFFRACTIONr_mcangle_other5.6996.9491937
X-RAY DIFFRACTIONr_scbond_it4.5595.1731499
X-RAY DIFFRACTIONr_scbond_other4.5575.1761500
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.7257.5322189
X-RAY DIFFRACTIONr_long_range_B_refined8.66553.9723270
X-RAY DIFFRACTIONr_long_range_B_other8.66753.9913266
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.323 73 -
Rwork0.218 1355 -
obs--100 %

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