[English] 日本語
Yorodumi
- PDB-7yzg: Crystal structure of the Xenopus FoxH1 bound to the TGTGGATT site -

+
Open data


ID or keywords:

Loading...

-
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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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

-
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)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more