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- PDB-7yzc: Crystal structure of the zebrafish FoxH1 bound to the TGTTTATT site -

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Basic information

Entry
Database: PDB / ID: 7yzc
TitleCrystal structure of the zebrafish FoxH1 bound to the TGTTTATT site
Components
  • DNA (5'-D(*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
  • DNA (5'-D(*TP*CP*TP*CP*AP*AP*TP*AP*AP*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
ACETATE ION / DNA / DNA (> 10) / Forkhead box protein H1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.17 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*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,3935
Polymers24,2753
Non-polymers1182
Water68538
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint-26 kcal/mol
Surface area10350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.183, 96.557, 153.812
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: 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*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')


Mass: 4967.250 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*AP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4825.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish)
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 38 / 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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 20% PEG Smear High (mix of PEG 6000, PEG 8000, PEG 10000), 0.1 M sodium acetate pH 4.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.17→76.91 Å / Num. obs: 12168 / % possible obs: 82.5 % / Redundancy: 6.3 % / CC1/2: 0.995 / Rpim(I) all: 0.055 / Net I/σ(I): 7.9
Reflection shellResolution: 2.172→2.336 Å / Num. unique obs: 608 / CC1/2: 0.552 / Rpim(I) all: 0.488 / % possible all: 44.7

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Processing

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

7yz7


Resolution: 2.17→76.91 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.934 / SU B: 16.233 / SU ML: 0.19 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.215 / 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
Rfree0.24136 604 5 %RANDOM
Rwork0.21039 ---
obs0.21202 11564 82.51 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.2 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å2-0 Å2
2---0.74 Å20 Å2
3----0.61 Å2
Refinement stepCycle: LAST / Resolution: 2.17→76.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms955 650 8 38 1651
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0151751
X-RAY DIFFRACTIONr_bond_other_d0.0020.0191316
X-RAY DIFFRACTIONr_angle_refined_deg1.2331.5472452
X-RAY DIFFRACTIONr_angle_other_deg1.2232.7443058
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4085114
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.90222.11552
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.64815173
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.876156
X-RAY DIFFRACTIONr_chiral_restr0.0710.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021470
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02382
X-RAY DIFFRACTIONr_mcbond_it1.6662.63464
X-RAY DIFFRACTIONr_mcbond_other1.6372.612461
X-RAY DIFFRACTIONr_mcangle_it2.5263.913574
X-RAY DIFFRACTIONr_mcangle_other2.5243.916575
X-RAY DIFFRACTIONr_scbond_it1.7832.8111287
X-RAY DIFFRACTIONr_scbond_other1.7832.8131288
X-RAY DIFFRACTIONr_scangle_other2.6984.2011879
X-RAY DIFFRACTIONr_long_range_B_refined4.45674.4255272
X-RAY DIFFRACTIONr_long_range_B_other4.4574.4325270
LS refinement shellResolution: 2.172→2.228 Å
RfactorNum. reflection% reflection
Rfree0.355 5 -
Rwork0.391 70 -
obs--6.83 %
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)
13.6844-0.4391-0.32213.85030.17346.8304-0.0907-0.0239-0.0496-0.02290.07660.1129-0.2011-0.34740.01410.0152-0.0285-0.00420.2723-0.00940.167-4.815-18.08626.607
22.4902-0.23650.1487.5703-0.27784.67660.00030.11310.0184-0.5681-0.0127-0.19450.0127-0.07910.01230.1828-0.07570.02770.29150.00250.1382-1.798-18.6412.367
32.2831-1.0818-0.01624.90640.01865.5485-0.11350.26090.1804-1.01980.11640.039-0.2585-0.3025-0.00290.2818-0.0816-0.03540.33360.00810.1831-3.297-17.69311.787
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A91 - 209
2X-RAY DIFFRACTION2B1 - 16
3X-RAY DIFFRACTION3C1 - 16

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