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- PDB-7yzd: Crystal structure of the zebrafish FoxH1 bound to the TGTTTACT si... -

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Basic information

Entry
Database: PDB / ID: 7yzd
TitleCrystal structure of the zebrafish FoxH1 bound to the TGTTTACT site (fkh motif GTAAACA)
Components
  • DNA (5'-D(*TP*CP*TP*CP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
  • DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-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 / TRIETHYLENE GLYCOL / DNA / DNA (> 10) / Forkhead box protein H1
Similarity search - Component
Biological speciesDanio rerio (zebrafish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.13 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(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-3')
C: DNA (5'-D(*TP*CP*TP*CP*AP*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4855
Polymers24,2763
Non-polymers2092
Water52229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4860 Å2
ΔGint-26 kcal/mol
Surface area10190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.241, 96.749, 150.809
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2

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Components

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Protein , 1 types, 1 molecules A

#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

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*CP*TP*GP*AP*GP*A)-3')


Mass: 4952.239 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*GP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')


Mass: 4841.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Danio rerio (zebrafish)

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Non-polymers , 3 types, 31 molecules

#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 29 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.72 Å3/Da / Density % sol: 54.82 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 25% PEG Smear High (mix of PEG 6000, PEG 8000, PEG 10000), 0.2 M lithium sulfate

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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 18, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.13→46.063 Å / Num. obs: 9559 / % possible obs: 63.7 % / Redundancy: 5.8 % / Biso Wilson estimate: 45.12 Å2 / CC1/2: 0.998 / Rpim(I) all: 0.043 / Net I/σ(I): 11.7
Reflection shellResolution: 2.144→2.329 Å / Redundancy: 4 % / Num. unique obs: 478 / CC1/2: 0.373 / % possible all: 14.9

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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: 2.13→46.06 Å / SU ML: 0.2603 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 34.2147
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.2525 479 5.02 %RANDOM
Rwork0.211 9058 --
obs0.2131 9537 62.63 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 53.67 Å2
Refinement stepCycle: LAST / Resolution: 2.13→46.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms925 650 14 29 1618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00561691
X-RAY DIFFRACTIONf_angle_d0.77652416
X-RAY DIFFRACTIONf_chiral_restr0.04261
X-RAY DIFFRACTIONf_plane_restr0.0058195
X-RAY DIFFRACTIONf_dihedral_angle_d25.7731679
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.13-2.440.2775650.28021063X-RAY DIFFRACTION22.69
2.44-3.080.32781570.27513253X-RAY DIFFRACTION67.73
3.08-46.060.23572570.19274742X-RAY DIFFRACTION95.75
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)
11.405926204280.2467437480581.108016094431.44974965054-1.19229566072.25669702365-0.215727121315-0.03462096906940.05996360867450.1122106543990.08015353302180.3262094813250.11713026776-0.175548916781-0.0001702652257250.243013935084-0.033004971816-0.01040032262260.2828852780150.01272402123750.270201298176-3.5670910039-23.78710779127.0834475493
21.328078536560.53507681214-0.09375705390970.312437215405-0.250628050290.7934871581290.0955656533683-0.9188776444771.423631668040.4346011642930.4472268461090.0857158207279-0.900552626557-0.1798872869560.1327779676940.232683216772-0.0224156654502-0.1973647583460.511554798617-0.0450651339668-0.03726148514761.36911198852-17.520734544629.1215868039
30.5597759831570.355602423106-0.9137232444741.760869983860.5431147959662.64056431788-0.0885969415631-0.0535854564667-0.352941415869-0.2048266248030.1948710848820.150424131622-0.148227833036-0.100355010343-0.0001126607614610.222402360347-0.0256986242036-0.02925422009280.3674682748910.06276832001670.32889673892-1.66839881015-21.360416125321.6660178427
40.0140070429808-0.006584700591460.003749848039310.0940613298502-0.06226898235310.0396294159860.3415966766390.07342759869120.1308290354880.1031380231930.2526111713350.352038205532-0.752383426062-1.49636306440.000515101372860.9470684122650.1985390901150.06129283528140.5357822408190.1763148074280.661923517796-9.11541907016-2.7833781709919.2820187861
50.2605195490070.0645260115228-0.1720116656650.181989049054-0.3855488727910.840857916725-0.1322322019960.8078424856121.027695907560.3072428820250.5974207485970.258640654154-0.490214098805-1.570078522990.05881149310730.4037578398650.0975160525694-0.02338480375880.709666985826-0.04899060758440.493859593061-14.5109313541-16.84415921226.399381355
60.4838081027840.02052479052360.691423426260.168399978839-0.01331272660221.07795693116-0.618627831532-0.2496624648-0.7459750786920.1514494426060.5277550360150.2647970750450.602021898906-0.318122607826-0.0004370535870690.44441782821-0.1215530929750.1266182024350.5221241359610.02792609795160.464370146919-8.23603370783-32.98353786330.6928178101
72.16308530063-0.08150744403250.9152163008591.8012306635-1.499875893861.48036920518-0.267656966126-0.7274398877260.0299743890978-1.125921311290.953449250119-2.46428619899-1.308612551981.27878783022-0.01509305126940.999989525287-0.4838836176930.2465719216640.3796072069550.112290698270.6925974017726.49473104359-7.5441261461412.7972740302
80.229856528237-0.166424691360.01395740232790.08689592182370.03501925838470.220832456398-0.2539890908540.7692351455860.213443634376-0.4431484610640.08875132015860.198010453691-0.261047590122-0.507387789029-0.0001059797670520.587315764946-0.098386862769-0.1792278459410.631642650128-0.02656806202520.554607978242-6.98295775501-18.54845456499.29819541069
97.178566250013.03444771596-3.156611690254.18287683538-3.838907026363.635472585210.5920994200470.00915688923891-2.41758939451-1.02866607839-1.11842515166-1.131893494591.504705873070.991802091846-0.05438075084420.880827345185-0.2007136925790.1086135092290.403461479409-0.1511499882910.663020001499-3.27989227744-37.385073214811.5114163689
100.004259308980160.04020208320160.02592325287950.1215198907650.1837254525130.4056261928210.228730926996-1.57739041470.418031343343-0.6223035889521.072604588820.07085445891530.09985969042-0.267999668155-0.009279830675491.20620045892-0.2337325011110.1890668369350.753573832271-0.02971889459570.554635896981-10.5759844721-44.211463478118.7978561342
110.583189890412-0.112638147686-0.1804677555960.4710397179790.4301789008080.348882051645-0.324481160984-0.52711312863-0.494546743197-1.572792497760.383465263230.5582652224570.629443556543-1.074790899410.03514612184230.889211852224-0.359344851543-0.1425421639460.4825218727720.0376659834110.600131148827-11.4591168396-38.127445865112.1054445826
120.238549870951-0.0980317658921-0.04943472815060.2153113904080.2468962731960.281938756747-0.4506037402290.0616704910295-0.0754511784997-0.7574976732960.0237602287212-0.9190353476140.08306577325790.281364237569-0.0009693131299570.459259883874-0.1729709310210.08787962860310.422402450337-0.006287511735620.350681668980.398352589036-24.950849277611.1205525032
130.712466107673-0.104461686680.4030582454940.1573603850420.1646214706430.3454693837060.164674144903-0.229594067951.3592854055-1.51644197939-0.2342182376280.162177655427-1.11248720331-0.704230357733-0.00177927266651.16439713682-0.146549215462-0.05960277287640.5109522300370.1559613785950.74473959643-0.642106510611-5.7064485593710.2043169892
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

IDRefine TLS-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11chain 'A' and (resid 92 through 119 )AA92 - 1191 - 28
22chain 'A' and (resid 120 through 130 )AA120 - 13029 - 39
33chain 'A' and (resid 131 through 158 )AA131 - 15840 - 67
44chain 'A' and (resid 159 through 170 )AA159 - 17068 - 79
55chain 'A' and (resid 171 through 178 )AA171 - 17880 - 87
66chain 'A' and (resid 179 through 208 )AA179 - 20888 - 112
77chain 'B' and (resid 1 through 5 )BB1 - 5
88chain 'B' and (resid 6 through 10 )BB6 - 10
99chain 'B' and (resid 11 through 15 )BB11 - 15
1010chain 'B' and (resid 16 through 16 )BB16
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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