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- PDB-7yzf: Crystal structure of the human FoxA2 bound to the TGTTTATT site (... -

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Basic information

Entry
Database: PDB / ID: 7yzf
TitleCrystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA)
Components
  • DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
  • Hepatocyte nuclear factor 3-beta
KeywordsDNA BINDING PROTEIN / transcription factor
Function / homology
Function and homology information


positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / dopaminergic neuron differentiation / Formation of axial mesoderm / Developmental Lineage of Pancreatic Acinar Cells ...positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / dopaminergic neuron differentiation / Formation of axial mesoderm / Developmental Lineage of Pancreatic Acinar Cells / positive regulation of gastrulation / cell fate specification / negative regulation of epithelial to mesenchymal transition / regulation of blood coagulation / Regulation of gene expression in beta cells / anatomical structure morphogenesis / adult locomotory behavior / negative regulation of DNA-binding transcription factor activity / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / cell junction / chromatin organization / nucleic acid binding / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / 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 / nucleus / cytoplasm
Similarity search - Function
Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. ...Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Hepatocyte nuclear factor 3-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsPluta, R. / Macias, M.J.
Funding support Spain, European Union, 2items
OrganizationGrant numberCountry
Ministry of Economy and Competitiveness (MINECO)BFU2017-82675-P Spain
H2020 Marie Curie Actions of the European Commission754510European Union
CitationJournal: Nat Commun / Year: 2022
Title: Molecular basis for DNA recognition by the maternal pioneer transcription factor FoxH1.
Authors: Pluta, R. / Aragon, E. / Prescott, N.A. / Ruiz, L. / Mees, R.A. / Baginski, B. / Flood, J.R. / Martin-Malpartida, P. / Massague, J. / David, Y. / Macias, M.J.
History
DepositionFeb 19, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 16, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 7, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 31, 2024Group: 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: DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
B: DNA (5'-D(P*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
C: Hepatocyte nuclear factor 3-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4844
Polymers24,4453
Non-polymers391
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.459, 92.695, 116.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: DNA chain DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')


Mass: 4967.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4825.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: Protein Hepatocyte nuclear factor 3-beta / HNF-3-beta / HNF-3B / Forkhead box protein A2 / Transcription factor 3B / TCF-3B


Mass: 14652.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA2, HNF3B, TCF3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y261
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / 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: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97926 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.179→58.421 Å / Num. obs: 9215 / % possible obs: 86.5 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rpim(I) all: 0.018 / Net I/σ(I): 19.9
Reflection shellResolution: 2.179→2.378 Å / Num. unique obs: 462 / CC1/2: 0.593 / Rpim(I) all: 0.544 / % possible all: 52.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YZE

7yze


Resolution: 2.18→58.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.039 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.268 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25728 901 9.8 %RANDOM
Rwork0.22188 ---
obs0.2254 8314 69.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0 Å2
2---0.19 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.18→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 656 1 5 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0151522
X-RAY DIFFRACTIONr_bond_other_d0.0010.021028
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.5012149
X-RAY DIFFRACTIONr_angle_other_deg1.3372.9632419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.2035.519245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49423.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63415119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.097155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_mcbond_it3.054.086343
X-RAY DIFFRACTIONr_mcbond_other3.034.077342
X-RAY DIFFRACTIONr_mcangle_it4.5486.132427
X-RAY DIFFRACTIONr_mcangle_other4.5466.142428
X-RAY DIFFRACTIONr_scbond_it3.5084.6661179
X-RAY DIFFRACTIONr_scbond_other3.4984.6621177
X-RAY DIFFRACTIONr_scangle_other4.9436.9961722
X-RAY DIFFRACTIONr_long_range_B_refined75047
X-RAY DIFFRACTIONr_long_range_B_other7.0025046
LS refinement shellResolution: 2.18→2.236 Å
RfactorNum. reflection% reflection
Rfree0.416 10 -
Rwork0.423 56 -
obs--6.67 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
14.5281-1.0095-0.750911.7441-0.11934.43950.12770.2072-0.455-0.2962-0.3920.41630.4576-0.02210.26430.11210.0903-0.02470.18930.01430.2044-21.302-11.662-17.26
25.9432-2.0516-0.249.48171.0993.30470.11260.092-0.51280.0412-0.38690.76230.3412-0.03090.27430.07430.07110.01570.19860.00970.1322-21.718-11.871-15.431
34.09611.0677-0.98232.67782.02025.941-0.0402-0.00090.1317-0.1932-0.0480.1108-0.37770.10550.08820.07060.090.02290.21890.07760.0453-9.845-2.225-16.209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2B1 - 16
3X-RAY DIFFRACTION3C153 - 238

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