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- PDB-7yza: Crystal structure of the zebrafish FoxH1 bound to the TGTGTATT site -

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Basic information

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


prechordal plate formation / axial mesoderm morphogenesis / specification of animal organ position / axial mesodermal cell fate specification / floor plate formation / lens placode formation involved in camera-type eye formation / Spemann organizer formation at the embryonic shield / floor plate development / somite rostral/caudal axis specification / embryonic heart tube left/right pattern formation ...prechordal plate formation / axial mesoderm morphogenesis / specification of animal organ position / axial mesodermal cell fate specification / floor plate formation / lens placode formation involved in camera-type eye formation / Spemann organizer formation at the embryonic shield / floor plate development / somite rostral/caudal axis specification / embryonic heart tube left/right pattern formation / mesendoderm development / endoderm formation / cell migration involved in gastrulation / notochord formation / notochord development / regulation of BMP signaling pathway / embryonic heart tube morphogenesis / brain morphogenesis / dorsal/ventral pattern formation / determination of left/right symmetry / blood vessel development / SMAD binding / heart looping / hypothalamus development / cellular response to cytokine stimulus / mesoderm formation / anatomical structure morphogenesis / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / regulation of gene expression / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / regulation of transcription by RNA polymerase II / chromatin / 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 speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.18 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

Downloads & links

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Assembly

Deposited unit
A: Forkhead box protein H1
B: DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*TP*AP*TP*TP*GP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*CP*AP*AP*TP*AP*CP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3154
Polymers24,2763
Non-polymers391
Water3,945219
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-22 kcal/mol
Surface area10790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.388, 29.917, 75.719
Angle α, β, γ (deg.)90.000, 108.250, 90.000
Int Tables number5
Space group name H-MC121

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Components

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


Mass: 14482.705 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Danio rerio (zebrafish) / Gene: foxh1, fast1, sur / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I9E1
#2: DNA chain DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*TP*AP*TP*TP*GP*AP*GP*A)-3')


Mass: 4992.263 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish)
#3: DNA chain DNA (5'-D(*TP*CP*TP*CP*AP*AP*TP*AP*CP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4801.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish)
#4: Chemical ChemComp-K / POTASSIUM ION


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


Mass: 18.015 Da / Num. of mol.: 219 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 41% PEG Smear LOW

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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: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 1.18→46.78 Å / Num. obs: 57653 / % possible obs: 85.1 % / Redundancy: 3.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.031 / Rpim(I) all: 0.02 / Rrim(I) all: 0.037 / Net I/σ(I): 15.4
Reflection shellResolution: 1.18→1.239 Å / Redundancy: 2.5 % / Num. unique obs: 3026 / CC1/2: 0.407 / Rpim(I) all: 0.627 / % possible all: 41.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7yz7

7yz7


Resolution: 1.18→46.78 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.978 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.04 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.148 2926 5.1 %RANDOM
Rwork0.1403 ---
obs0.1407 54975 82.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 60.21 Å2 / Biso mean: 16.526 Å2 / Biso min: 5.66 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å2-0 Å2-0.89 Å2
2--0.15 Å2-0 Å2
3---0.4 Å2
Refinement stepCycle: final / Resolution: 1.18→46.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1010 650 1 219 1880
Biso mean--11.61 25.18 -
Num. residues----154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0141782
X-RAY DIFFRACTIONr_bond_other_d0.0410.021390
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.5462549
X-RAY DIFFRACTIONr_angle_other_deg2.0542.7613238
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3875127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.91922.67956
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.18315195
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.398156
X-RAY DIFFRACTIONr_chiral_restr0.0990.2247
X-RAY DIFFRACTIONr_gen_planes_refined0.0170.021554
X-RAY DIFFRACTIONr_gen_planes_other0.0190.02400
X-RAY DIFFRACTIONr_rigid_bond_restr5.10231782
LS refinement shellResolution: 1.181→1.212 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 47 -
Rwork0.307 795 -
all-842 -
obs--16.46 %

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