[English] 日本語
Yorodumi
- PDB-7yzf: Crystal structure of the human FoxA2 bound to the TGTTTATT site (... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7yzf
TitleCrystal structure of the human FoxA2 bound to the TGTTTATT site (forkhead motif ATAAACA)
Components
  • DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
  • DNA (5'-D(P*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
  • Hepatocyte nuclear factor 3-beta
KeywordsDNA BINDING PROTEIN / transcription factor
Function / homology
Function and homology information


negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / positive regulation of transcription from RNA polymerase II promoter by glucose / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm ...negative regulation of transcription from RNA polymerase II promoter by glucose / negative regulation of glucokinase activity / positive regulation of cell-cell adhesion mediated by cadherin / primitive streak formation / positive regulation of embryonic development / positive regulation of transcription from RNA polymerase II promoter by glucose / response to interleukin-6 / endocrine pancreas development / regulation of insulin secretion involved in cellular response to glucose stimulus / Formation of definitive endoderm / positive regulation of gastrulation / Formation of axial mesoderm / dopaminergic neuron differentiation / negative regulation of epithelial to mesenchymal transition / cell fate specification / regulation of blood coagulation / Regulation of gene expression in beta cells / anatomical structure morphogenesis / adult locomotory behavior / negative regulation of DNA-binding transcription factor activity / sequence-specific double-stranded DNA binding / cell junction / chromatin organization / nucleic acid 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 / DNA-binding transcription factor activity / protein domain specific binding / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / Fork head domain / Forkhead domain / Fork head domain profile. ...Forkhead box protein, C-terminal / HNF3 C-terminal domain / Fork-head N-terminal / Forkhead N-terminal region / : / Fork head domain conserved site1 / Fork head domain signature 1. / 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) / Hepatocyte nuclear factor 3-beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 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: DNA (5'-D(P*AP*GP*AP*TP*TP*GP*TP*TP*TP*AP*TP*TP*GP*AP*GP*A)-3')
B: DNA (5'-D(P*TP*CP*TP*CP*AP*AP*TP*AP*AP*AP*CP*AP*AP*TP*CP*T)-3')
C: Hepatocyte nuclear factor 3-beta
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,4844
Polymers24,4453
Non-polymers391
Water905
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-27 kcal/mol
Surface area10310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.459, 92.695, 116.842
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

-
Components

#1: DNA chain DNA (5'-D(P*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.) Homo sapiens (human)
#2: DNA chain DNA (5'-D(P*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.) Homo sapiens (human)
#3: Protein Hepatocyte nuclear factor 3-beta / HNF-3-beta / HNF-3B / Forkhead box protein A2 / Transcription factor 3B / TCF-3B


Mass: 14652.791 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FOXA2, HNF3B, TCF3B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y261
#4: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.14 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 25% PEG 3350, 0.1 M Bis-Tris pH 5.5

-
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: Feb 1, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97926 Å / Relative weight: 1
ReflectionResolution: 2.179→58.421 Å / Num. obs: 9215 / % possible obs: 86.5 % / Redundancy: 9.9 % / CC1/2: 0.998 / Rpim(I) all: 0.018 / Net I/σ(I): 19.9
Reflection shellResolution: 2.179→2.378 Å / Num. unique obs: 462 / CC1/2: 0.593 / Rpim(I) all: 0.544 / % possible all: 52.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
autoPROCdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YZE

7yze


Resolution: 2.18→58.42 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.933 / SU B: 18.039 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.401 / ESU R Free: 0.268 / 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
Rfree0.25728 901 9.8 %RANDOM
Rwork0.22188 ---
obs0.2254 8314 69.23 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å / Solvent model: MASK
Displacement parametersBiso mean: 72.04 Å2
Baniso -1Baniso -2Baniso -3
1-0.74 Å20 Å2-0 Å2
2---0.19 Å20 Å2
3----0.54 Å2
Refinement stepCycle: LAST / Resolution: 2.18→58.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms726 656 1 5 1388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0151522
X-RAY DIFFRACTIONr_bond_other_d0.0010.021028
X-RAY DIFFRACTIONr_angle_refined_deg1.1731.5012149
X-RAY DIFFRACTIONr_angle_other_deg1.3372.9632419
X-RAY DIFFRACTIONr_dihedral_angle_1_deg21.2035.519245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.49423.52934
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63415119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.097155
X-RAY DIFFRACTIONr_chiral_restr0.0830.2198
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021191
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_mcbond_it3.054.086343
X-RAY DIFFRACTIONr_mcbond_other3.034.077342
X-RAY DIFFRACTIONr_mcangle_it4.5486.132427
X-RAY DIFFRACTIONr_mcangle_other4.5466.142428
X-RAY DIFFRACTIONr_scbond_it3.5084.6661179
X-RAY DIFFRACTIONr_scbond_other3.4984.6621177
X-RAY DIFFRACTIONr_scangle_other4.9436.9961722
X-RAY DIFFRACTIONr_long_range_B_refined75047
X-RAY DIFFRACTIONr_long_range_B_other7.0025046
LS refinement shellResolution: 2.18→2.236 Å
RfactorNum. reflection% reflection
Rfree0.416 10 -
Rwork0.423 56 -
obs--6.67 %
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)
14.5281-1.0095-0.750911.7441-0.11934.43950.12770.2072-0.455-0.2962-0.3920.41630.4576-0.02210.26430.11210.0903-0.02470.18930.01430.2044-21.302-11.662-17.26
25.9432-2.0516-0.249.48171.0993.30470.11260.092-0.51280.0412-0.38690.76230.3412-0.03090.27430.07430.07110.01570.19860.00970.1322-21.718-11.871-15.431
34.09611.0677-0.98232.67782.02025.941-0.0402-0.00090.1317-0.1932-0.0480.1108-0.37770.10550.08820.07060.090.02290.21890.07760.0453-9.845-2.225-16.209
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 16
2X-RAY DIFFRACTION2B1 - 16
3X-RAY DIFFRACTION3C153 - 238

+
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://pdbjlc1.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