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- PDB-7yzb: Crystal structure of the human FoxH1 bound to the TGTGGATT site -

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Basic information

Entry
Database: PDB / ID: 7yzb
TitleCrystal structure of the human FoxH1 bound to the TGTGGATT site
Components
  • DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*CP*GP*A)-3')
  • DNA (5'-D(*TP*CP*GP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*T)-3')
  • Forkhead box protein H1
KeywordsDNA BINDING PROTEIN / transcription factor
Function / homology
Function and homology information


activin responsive factor complex / secondary heart field specification / embryonic heart tube anterior/posterior pattern specification / nodal signaling pathway / cardiac right ventricle morphogenesis / co-SMAD binding / aorta morphogenesis / determination of left/right asymmetry in lateral mesoderm / bHLH transcription factor binding / negative regulation of intracellular estrogen receptor signaling pathway ...activin responsive factor complex / secondary heart field specification / embryonic heart tube anterior/posterior pattern specification / nodal signaling pathway / cardiac right ventricle morphogenesis / co-SMAD binding / aorta morphogenesis / determination of left/right asymmetry in lateral mesoderm / bHLH transcription factor binding / negative regulation of intracellular estrogen receptor signaling pathway / negative regulation of androgen receptor signaling pathway / Germ layer formation at gastrulation / hepatocyte differentiation / axial mesoderm development / ventricular trabecula myocardium morphogenesis / Signaling by Activin / Formation of axial mesoderm / Signaling by NODAL / nuclear androgen receptor binding / heart looping / cellular response to cytokine stimulus / SMAD binding / outflow tract morphogenesis / R-SMAD binding / cis-regulatory region sequence-specific DNA binding / transforming growth factor beta receptor signaling pathway / negative regulation of DNA-binding transcription factor activity / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / transcription regulator complex / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / protein domain specific binding / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / nucleus
Similarity search - Function
: / : / Fork head domain / Forkhead domain / Fork head domain profile. / FORKHEAD / Fork head domain conserved site 2 / Fork head domain signature 2. / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
: / DNA / DNA (> 10) / Forkhead box protein H1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.47 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: Forkhead box protein H1
B: DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*CP*GP*A)-3')
C: DNA (5'-D(*TP*CP*GP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4134
Polymers30,3743
Non-polymers391
Water2,738152
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4620 Å2
ΔGint-22 kcal/mol
Surface area11370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.118, 78.029, 51.879
Angle α, β, γ (deg.)90.000, 100.460, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Forkhead box protein H1 / Forkhead activin signal transducer 1 / Fast-1 / hFAST-1 / Forkhead activin signal transducer 2 / Fast-2


Mass: 20578.701 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXH1, FAST1, FAST2 / Production host: Escherichia coli (E. coli) / References: UniProt: O75593
#2: DNA chain DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*CP*GP*A)-3')


Mass: 4993.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#3: DNA chain DNA (5'-D(*TP*CP*GP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4802.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#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.: 152 / 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: 2.37 Å3/Da / Density % sol: 48.03 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3 / Details: 18% PEG 3350, 0.2 M ammonium chloride pH 6.3

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979257 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979257 Å / Relative weight: 1
ReflectionResolution: 1.47→51.02 Å / Num. obs: 36550 / % possible obs: 100 % / Redundancy: 15 % / CC1/2: 0.997 / Rmerge(I) obs: 0.104 / Rpim(I) all: 0.027 / Rrim(I) all: 0.108 / Net I/σ(I): 19.1
Reflection shellResolution: 1.471→1.618 Å / Redundancy: 14.7 % / Num. unique obs: 1800 / CC1/2: 0.912 / R split: 1.5 / Rpim(I) all: 0.454 / % possible all: 50.6

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Processing

Software
NameVersionClassification
Aimless0.7.4data scaling
REFMAC5.8.0267refinement
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YZ7

7yz7


Resolution: 1.47→51.02 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.969 / SU B: 3.843 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.086 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1905 1771 4.8 %RANDOM
Rwork0.1621 ---
obs0.1636 34784 75.94 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso max: 90.39 Å2 / Biso mean: 39.719 Å2 / Biso min: 16.12 Å2
Baniso -1Baniso -2Baniso -3
1--1.13 Å20 Å20.4 Å2
2---0.83 Å2-0 Å2
3---1.7 Å2
Refinement stepCycle: final / Resolution: 1.47→51.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1037 650 1 152 1840
Biso mean--57.88 41.82 -
Num. residues----157
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0141835
X-RAY DIFFRACTIONr_bond_other_d0.0010.0191447
X-RAY DIFFRACTIONr_angle_refined_deg1.441.5542624
X-RAY DIFFRACTIONr_angle_other_deg1.2832.643343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6225131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.97218.45171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37315190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1891516
X-RAY DIFFRACTIONr_chiral_restr0.0830.2249
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021628
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02454
X-RAY DIFFRACTIONr_rigid_bond_restr2.62733282
LS refinement shellResolution: 1.47→1.508 Å / Rfactor Rfree error: 0 /
RfactorNum. reflection
Rfree0.174 5

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