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- PDB-8j0l: Structure of DNA binding Domain of Human TFAP2A -

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Basic information

Entry
Database: PDB / ID: 8j0l
TitleStructure of DNA binding Domain of Human TFAP2A
ComponentsTranscription factor AP-2-alpha
KeywordsDNA BINDING PROTEIN / TFAP2 family
Function / homology
Function and homology information


optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / nuclear receptor corepressor activity / trigeminal nerve development / TFAP2 (AP-2) family regulates transcription of other transcription factors / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / retina layer formation / TFAP2 (AP-2) family regulates transcription of cell cycle factors ...optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / nuclear receptor corepressor activity / trigeminal nerve development / TFAP2 (AP-2) family regulates transcription of other transcription factors / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / retina layer formation / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Negative regulation of activity of TFAP2 (AP-2) family transcription factors / Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors / negative regulation of transcription by competitive promoter binding / Activation of the TFAP2 (AP-2) family of transcription factors / anatomical structure development / embryonic cranial skeleton morphogenesis / embryonic forelimb morphogenesis / bone morphogenesis / inner ear morphogenesis / roof of mouth development / eyelid development in camera-type eye / regulation of cell differentiation / SUMOylation of transcription factors / negative regulation of reactive oxygen species metabolic process / positive regulation of bone mineralization / TFAP2 (AP-2) family regulates transcription of growth factors and their receptors / kidney development / sensory perception of sound / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to iron ion / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of apoptotic process / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / identical protein binding / nucleus
Similarity search - Function
Transcription factor AP-2 alpha, N-terminal / Transcription factor AP-2 / Transcription factor AP-2, C-terminal / Transcription factor AP-2
Similarity search - Domain/homology
Transcription factor AP-2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsLiu, K. / Xiao, Y.Q. / Gan, L.Y. / 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
Revision 1.3Sep 20, 2023Group: Refinement description / Category: pdbx_initial_refinement_model
Item: _pdbx_initial_refinement_model.source_name / _pdbx_initial_refinement_model.type

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)47,8234
Polymers47,6392
Non-polymers1842
Water3,459192
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-63 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.613, 81.907, 115.939
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-alpha / AP2-alpha / AP-2 transcription factor / Activating enhancer-binding protein 2-alpha / Activator ...AP2-alpha / AP-2 transcription factor / Activating enhancer-binding protein 2-alpha / Activator protein 2 / AP-2


Mass: 23819.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TFAP2A, AP2TF, TFAP2 / Cell (production host): plasmid / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P05549
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 192 / 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: 2.52 Å3/Da / Density % sol: 51.23 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Sodium tartrate dibasic dihydrate, 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: BL10U2 / Wavelength: 0.97918 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 1.97→66.9 Å / Num. obs: 34109 / % possible obs: 98.6 % / Redundancy: 4.7 % / CC1/2: 0.998 / Net I/σ(I): 15.9
Reflection shellResolution: 1.97→2.08 Å / Num. unique obs: 4928 / CC1/2: 0.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→19.32 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.778 / SU ML: 0.103 / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.137 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21905 1668 4.9 %RANDOM
Rwork0.18255 ---
obs0.18441 32336 98.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.951 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å2-0 Å2
2--0.01 Å2-0 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.98→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2904 0 12 193 3109
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132956
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172843
X-RAY DIFFRACTIONr_angle_refined_deg1.6161.6453990
X-RAY DIFFRACTIONr_angle_other_deg1.3971.5746604
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0055368
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.33821.895153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6515520
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3711524
X-RAY DIFFRACTIONr_chiral_restr0.080.2385
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023245
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02575
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_it2.3982.8641499
X-RAY DIFFRACTIONr_mcbond_other2.3962.8631498
X-RAY DIFFRACTIONr_mcangle_it3.4494.2581858
X-RAY DIFFRACTIONr_mcangle_other3.4484.2591859
X-RAY DIFFRACTIONr_scbond_it3.2933.2691457
X-RAY DIFFRACTIONr_scbond_other3.2923.2711458
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8124.7442133
X-RAY DIFFRACTIONr_long_range_B_refined6.18234.6063311
X-RAY DIFFRACTIONr_long_range_B_other6.14834.4373274
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.026 Å
RfactorNum. reflection% reflection
Rfree0.273 101 -
Rwork0.251 2375 -
obs--99.2 %

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