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- PDB-7yzg: Crystal structure of the Xenopus FoxH1 bound to the TGTGGATT site -

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Basic information

Entry
Database: PDB / ID: 7yzg
TitleCrystal structure of the Xenopus FoxH1 bound to the TGTGGATT site
Components
  • DNA (5'-D(*CP*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*AP*G)-3')
  • DNA (5'-D(*CP*TP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*TP*G)-3')
  • Forkhead box protein H1
KeywordsDNA BINDING PROTEIN / transcription factor
Function / homology
Function and homology information


mesodermal cell fate specification / activin responsive factor complex / activin receptor signaling pathway / gastrulation with mouth forming second / SMAD binding / cellular response to cytokine stimulus / transforming growth factor beta receptor signaling pathway / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription cis-regulatory region binding ...mesodermal cell fate specification / activin responsive factor complex / activin receptor signaling pathway / gastrulation with mouth forming second / SMAD binding / cellular response to cytokine stimulus / transforming growth factor beta receptor signaling pathway / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription cis-regulatory region binding / DNA-binding transcription factor activity / positive regulation of DNA-templated transcription / 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 speciesXenopus laevis (African clawed frog)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.82 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(*CP*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*AP*G)-3')
C: DNA (5'-D(*CP*TP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*TP*G)-3')


Theoretical massNumber of molelcules
Total (without water)26,0873
Polymers26,0873
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.304, 78.726, 103.253
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Forkhead box protein H1 / Forkhead activin signal transducer 1 / Fast-1 / xFAST-1 / XFoxH1a


Mass: 16291.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: foxh1, fast-1, fast1, foxh1a / Production host: Escherichia coli (E. coli) / References: UniProt: P70056
#2: DNA chain DNA (5'-D(*CP*AP*GP*AP*TP*TP*GP*TP*GP*GP*AP*TP*TP*GP*AP*G)-3')


Mass: 4993.250 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog)
#3: DNA chain DNA (5'-D(*CP*TP*CP*AP*AP*TP*CP*CP*AP*CP*AP*AP*TP*CP*TP*G)-3')


Mass: 4802.144 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Xenopus laevis (African clawed frog)

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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: 3.61 Å3/Da / Density % sol: 65.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 30% PEG 8000, 0.2 M ammonium sulfate, 0.1 sodium cacodylate

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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: 2.82→62.6 Å / Num. obs: 5547 / % possible obs: 90.8 % / Redundancy: 14.7 % / Biso Wilson estimate: 56.89 Å2 / CC1/2: 0.997 / Rpim(I) all: 0.083 / Net I/σ(I): 8.2
Reflection shellResolution: 2.822→3.095 Å / Num. unique obs: 234 / CC1/2: 0.484 / % possible all: 68

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7yz7

7yz7


Resolution: 2.82→62.6 Å / SU ML: 0.3849 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 17.5457
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2554 270 4.87 %
Rwork0.1996 5271 -
obs0.2022 5541 57.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 67.87 Å2
Refinement stepCycle: LAST / Resolution: 2.82→62.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms989 650 0 0 1639
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00461744
X-RAY DIFFRACTIONf_angle_d0.75542494
X-RAY DIFFRACTIONf_chiral_restr0.0418270
X-RAY DIFFRACTIONf_plane_restr0.0064207
X-RAY DIFFRACTIONf_dihedral_angle_d29.2398446
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.82-3.550.3214590.28311076X-RAY DIFFRACTION24.16
3.56-62.60.24662110.18784195X-RAY DIFFRACTION90.4
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)
10.5447085542890.03883851822730.06991316447550.3377598903110.03987769907280.033563798145-0.0668104689749-0.01508794209821.11187777543-0.2431528487180.373847468817-0.216296638555-0.0443724019987-0.170532709273-0.008662421192630.4456682168060.1186454543970.08026111756850.616856304830.05915349019810.54301307443422.4461542263-0.288875690453-10.4170761172
20.09893234584260.244790104796-0.06551927877560.639780162740.3051116542930.5736953330680.2125205111760.0918899227806-0.8023004300110.335745972589-0.605446734709-0.739712071032-0.6749871106170.407276619593-0.08096090164080.294448447443-0.041594636473-0.06703813805740.2313277428470.08037619008380.36366130945724.2524332671-14.04703853311.30325615743
30.495631454644-0.240432013543-0.428561014110.1850047516280.1112907714620.9601606823410.484415855009-0.428678869419-0.1981289027250.800302923817-0.714517620656-0.84671334334-0.3008187765220.570355293352-0.5624720685170.316225873722-1.007731869460.161616557273-0.8532693762040.07201710348920.66676502031826.7368383466-6.130013819953.42343006757
40.211135784945-0.285541918619-0.295685682240.3377333090920.3302003449390.5153454603770.056333405037-0.5800199498531.73635824398-0.04059270231120.154054610648-0.765242604313-1.080443594680.8097276889210.01922599705751.15789707163-0.1029670164240.2748111858280.5035231218540.06913026875221.1362088081126.62809169533.15212456169-3.01105731269
50.3695049459820.221639689644-0.5648134737481.00950368814-0.3122692646920.8069136403370.233640441817-0.4470466135780.000134110639686-0.245187155028-0.537394564273-0.2820733471510.221760806129-0.595461169463-0.05140902945040.245529059871-0.03301234572-0.08998353848960.428557149879-0.001515412588370.34119030713914.0073965449-10.86793657636.84168135808
60.447200791868-0.1602670301630.03596862546260.7994838949120.8188455348410.6911909028410.13912522341-0.02771585233760.0103787237682-0.0888819329303-0.402005086751-0.212173151592-0.1767185705660.874328163194-0.001837139647810.283644195830.0527520094706-0.005795687899190.5841513308060.08191857681950.44104029818223.5862788832-10.7014034292-12.8797819865
70.09782662159740.177371192411-0.2582398735630.470625722341-0.6774222938141.138228252420.124368038886-0.2040604210070.1493343039920.694231815634-0.621810627430.08812476307490.03882103959970.951430593318-0.07635612046630.3985037015740.01605413160860.2410686151050.46006198155-0.1099008084710.51479907496331.1841752884-18.1562710527-8.63274645306
80.003509545510190.02381509722510.002518585166920.09214078812140.06045681313930.04390014431040.5892413807050.4907610910641.301706464350.6125202045290.579300176555-0.603387715416-0.657706614084-0.3008973052030.001479053490760.8442631272390.03296154572030.2202737520570.639816973716-0.1378891174270.70742489684413.95229558374.9027667688418.8526584021
90.6719034031350.0943670497712-0.4547990158240.0641543681072-0.2162701298040.5529050254530.927059739185-0.1807811907971.1913413473-0.435136911839-0.7696727951930.558912481142-1.774090562830.01577319041330.04677520612110.578151336460.155478251078-0.1729111186020.703751492546-0.07653734815110.4325132229837.80016990338-4.689068824134.66740184023
102.552318733071.074721937852.324163494640.5703272434760.6193173816364.96676681244-0.144187471992-0.1341045347441.0979155937-0.231785887460.0784942177546-0.712817387063-0.584926115134-1.05914593324-0.4547306625830.951981364750.3079605907760.01162833912460.3411443510760.4756777765651.230659274748.487643099372.81587845607-13.8121698712
110.3121339445930.0418020099394-0.2116127653240.00365355708317-0.09890664462680.181620704253-0.6425070760310.675677522686-0.1085240918590.2670885976860.975232798381.508192221360.628810598063-0.739424151792-0.02963858152920.66494348466-0.00175565279029-0.005307505851470.7577016015490.2464589664630.7024485813748.97150762058-4.33366591189-15.0594247678
120.3456555446210.1932543624710.3383498926340.1120126170310.1675896179040.3705183233850.6768677025230.03850408562942.041224940370.245759808817-0.2543287873230.199567698107-0.966503952018-0.646347669898-0.05043228731241.254279084350.3362086139070.1844743133730.643695615244-0.04282570811870.9838685078768.302358346414.51216309820.564603664637
130.0146379762646-0.109603805736-0.03444537236080.4608625232980.1904372123750.06009364118370.2245948435930.0415451211110.3629178481210.4855399232110.161568914394-0.212800854986-1.69959970996-0.4834482128720.0001043934381810.6896181419540.009011317344750.0454714989350.919920194875-0.1335827012420.52813700589711.7884936171-2.2083704338318.4036229656
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 114 through 121 )AA114 - 1211 - 8
22chain 'A' and (resid 122 through 139 )AA122 - 1399 - 26
33chain 'A' and (resid 140 through 150 )AA140 - 15027 - 37
44chain 'A' and (resid 151 through 160 )AA151 - 16038 - 47
55chain 'A' and (resid 161 through 191 )AA161 - 19148 - 78
66chain 'A' and (resid 192 through 223 )AA192 - 22379 - 110
77chain 'A' and (resid 224 through 234 )AA224 - 234111 - 121
88chain 'B' and (resid 1 through 5 )BB1 - 5
99chain 'B' and (resid 6 through 10 )BB6 - 10
1010chain 'B' and (resid 11 through 16 )BB11 - 16
1111chain 'C' and (resid 1 through 5 )CC1 - 5
1212chain 'C' and (resid 6 through 10 )CC6 - 10
1313chain 'C' and (resid 11 through 16 )CC11 - 16

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