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- PDB-8j0r: Structure of human TFAP2A in complex with DNA -

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Basic information

Entry
Database: PDB / ID: 8j0r
TitleStructure of human TFAP2A in complex with DNA
Components
  • DNA (5'-D(*CP*TP*GP*CP*CP*TP*CP*AP*GP*GP*CP*AP*C)-3')
  • DNA (5'-D(*GP*TP*GP*CP*CP*TP*GP*AP*GP*GP*CP*AP*G)-3')
  • Transcription factor AP-2-alpha
KeywordsDNA BINDING PROTEIN/DNA / TFAP2 family / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / 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 / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Specification of the neural plate border / retina layer formation ...optic vesicle morphogenesis / optic cup structural organization / oculomotor nerve formation / positive regulation of tooth mineralization / 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 / TFAP2 (AP-2) family regulates transcription of cell cycle factors / Specification of the neural plate border / retina layer formation / 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 / embryonic cranial skeleton morphogenesis / bone morphogenesis / embryonic forelimb morphogenesis / inner ear morphogenesis / eyelid development in camera-type eye / Regulation of MITF-M-dependent genes involved in pigmentation / roof of mouth development / 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 / skeletal system development / RNA polymerase II transcription regulatory region sequence-specific DNA binding / cellular response to iron ion / sensory perception of sound / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / positive regulation of neuron apoptotic process / nervous system development / regulation of cell population proliferation / DNA-binding transcription activator activity, RNA polymerase II-specific / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / negative regulation of apoptotic process / chromatin / 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
DI(HYDROXYETHYL)ETHER / GUANIDINE-3-PROPANOL / DNA / DNA (> 10) / Transcription factor AP-2-alpha
Similarity search - Component
Biological speciesHomo sapiens (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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-alpha
B: Transcription factor AP-2-alpha
C: DNA (5'-D(*CP*TP*GP*CP*CP*TP*CP*AP*GP*GP*CP*AP*C)-3')
D: DNA (5'-D(*GP*TP*GP*CP*CP*TP*GP*AP*GP*GP*CP*AP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,86915
Polymers55,5844
Non-polymers1,28511
Water6,431357
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12540 Å2
ΔGint-85 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.790, 124.790, 96.917
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#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 / Production host: Escherichia coli (E. coli) / References: UniProt: P05549

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA (5'-D(*CP*TP*GP*CP*CP*TP*CP*AP*GP*GP*CP*AP*C)-3')


Mass: 3912.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*TP*GP*CP*CP*TP*GP*AP*GP*GP*CP*AP*G)-3')


Mass: 4032.622 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 368 molecules

#4: Chemical ChemComp-PG3 / GUANIDINE-3-PROPANOL


Mass: 118.158 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12N3O
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 357 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.92 Å3/Da / Density % sol: 68.62 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.1 M citric acid (pH3.5), 34% PEG 200 (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: 2.1→108.1 Å / Num. obs: 51127 / % possible obs: 100 % / Redundancy: 9.1 % / CC1/2: 0.998 / Net I/σ(I): 15
Reflection shellResolution: 2.1→2.16 Å / Num. unique obs: 4160 / CC1/2: 0.825

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Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata scaling
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.99 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 2.972 / SU ML: 0.079 / Cross valid method: THROUGHOUT / ESU R: 0.127 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19411 2688 5.3 %RANDOM
Rwork0.16213 ---
obs0.1638 48346 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.284 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å2-0.01 Å2-0 Å2
2---0.01 Å20 Å2
3---0.04 Å2
Refinement stepCycle: 1 / Resolution: 2.1→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3243 527 85 359 4214
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0123959
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173557
X-RAY DIFFRACTIONr_angle_refined_deg1.7891.5645432
X-RAY DIFFRACTIONr_angle_other_deg1.4941.6918277
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6025422
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97921.377167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.06115588
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5111528
X-RAY DIFFRACTIONr_chiral_restr0.0950.2507
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024002
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02799
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_it3.1683.2121694
X-RAY DIFFRACTIONr_mcbond_other3.1653.2091693
X-RAY DIFFRACTIONr_mcangle_it3.9944.7912114
X-RAY DIFFRACTIONr_mcangle_other3.9944.7952115
X-RAY DIFFRACTIONr_scbond_it4.8613.8352265
X-RAY DIFFRACTIONr_scbond_other4.8613.8352264
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.915.5223319
X-RAY DIFFRACTIONr_long_range_B_refined8.39839.3294674
X-RAY DIFFRACTIONr_long_range_B_other8.34438.9014596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.1→2.155 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 184 -
Rwork0.213 3578 -
obs--99.95 %

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