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- PDB-7yz7: Crystal structure of the zebrafish FoxH1 bound to the TGTGGATT site -

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Basic information

Entry
Database: PDB / ID: 7yz7
TitleCrystal structure of the zebrafish FoxH1 bound to the TGTGGATT site
Components
  • DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*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


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 / hypothalamus development / blood vessel development / SMAD binding / cellular response to cytokine stimulus / heart looping / 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 / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / 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: 0.98 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 18, 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*GP*AP*TP*TP*GP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3164
Polymers24,2773
Non-polymers391
Water6,485360
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4870 Å2
ΔGint-26 kcal/mol
Surface area10470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)100.121, 30.093, 76.656
Angle α, β, γ (deg.)90.000, 108.690, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y

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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*GP*AP*TP*TP*GP*AP*GP*A)-3')


Mass: 5017.275 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*CP*CP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4777.131 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.: 360 / 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: 2.25 Å3/Da / Density % sol: 45.4 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 35% 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: 0.97928 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 21, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionResolution: 0.98→47.28 Å / Num. obs: 111474 / % possible obs: 89.9 % / Redundancy: 6.1 % / Biso Wilson estimate: 12.25 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.042 / Rpim(I) all: 0.018 / Rrim(I) all: 0.046 / Net I/σ(I): 17.7
Reflection shellResolution: 0.982→0.999 Å / Redundancy: 3.7 % / Num. unique obs: 1261 / CC1/2: 0.365 / Rpim(I) all: 0.68 / % possible all: 31.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimless0.6.2data scaling
PDB_EXTRACT3.27data extraction
autoPROCdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2c6y

2c6y


Resolution: 0.98→47.23 Å / SU ML: 0.0793 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 13.79
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1414 5530 4.96 %RANDOM
Rwork0.1323 105940 --
obs0.1328 111470 89.86 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 19.27 Å2
Refinement stepCycle: LAST / Resolution: 0.98→47.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms988 650 1 360 1999
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01281842
X-RAY DIFFRACTIONf_angle_d1.44652661
X-RAY DIFFRACTIONf_chiral_restr0.0914295
X-RAY DIFFRACTIONf_plane_restr0.0153224
X-RAY DIFFRACTIONf_dihedral_angle_d27.3946503
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.98-0.990.2948300.2868665X-RAY DIFFRACTION17.01
0.99-10.31560.2881210X-RAY DIFFRACTION30.48
1-1.020.286800.26631696X-RAY DIFFRACTION44.32
1.02-1.030.26471180.25432241X-RAY DIFFRACTION57.48
1.03-1.040.24681190.23392759X-RAY DIFFRACTION69.55
1.04-1.060.22131730.21013109X-RAY DIFFRACTION80.8
1.06-1.070.21571940.20163796X-RAY DIFFRACTION96.03
1.07-1.090.25032060.20243915X-RAY DIFFRACTION100
1.09-1.110.17382200.1683863X-RAY DIFFRACTION100
1.11-1.120.16921840.14143936X-RAY DIFFRACTION100
1.12-1.140.13842270.13133891X-RAY DIFFRACTION99.98
1.14-1.160.152060.11953896X-RAY DIFFRACTION100
1.16-1.190.12051990.11333926X-RAY DIFFRACTION100
1.19-1.210.13122300.10743893X-RAY DIFFRACTION100
1.21-1.240.11641880.10783912X-RAY DIFFRACTION100
1.24-1.270.12552030.10763919X-RAY DIFFRACTION100
1.27-1.30.12761850.11253956X-RAY DIFFRACTION100
1.3-1.330.11382090.11253896X-RAY DIFFRACTION100
1.33-1.370.12852130.11463972X-RAY DIFFRACTION100
1.37-1.420.13952240.11313863X-RAY DIFFRACTION100
1.42-1.470.15011800.10823917X-RAY DIFFRACTION100
1.47-1.530.12382150.10483932X-RAY DIFFRACTION99.93
1.53-1.590.11651910.10453979X-RAY DIFFRACTION99.98
1.59-1.680.10752040.10783948X-RAY DIFFRACTION99.98
1.68-1.780.12722160.11453910X-RAY DIFFRACTION99.83
1.78-1.920.13992320.12513932X-RAY DIFFRACTION99.86
1.92-2.110.15542060.13513950X-RAY DIFFRACTION99.76
2.11-2.420.13312060.13253954X-RAY DIFFRACTION99.66
2.42-3.050.17462050.14534011X-RAY DIFFRACTION99.55
3.05-47.230.13172110.14164093X-RAY DIFFRACTION99.24

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