[English] 日本語
Yorodumi
- PDB-3dfx: Opposite GATA DNA binding -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3dfx
TitleOpposite GATA DNA binding
Components
  • DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')
  • DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')
  • Trans-acting T-cell-specific transcription factor GATA-3
KeywordsTranscription/DNA / Activator / DNA-binding / Metal-binding / Nucleus / Transcription / Transcription regulation / Zinc / Zinc-finger / Transcription-DNA COMPLEX
Function / homology
Function and homology information


nephric duct formation / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureter morphogenesis / thymic T cell selection / ureteric bud formation ...nephric duct formation / : / regulation of cellular response to X-ray / : / : / type IV hypersensitivity / regulation of CD4-positive, alpha-beta T cell differentiation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of thyroid hormone generation / positive regulation of ureteric bud formation / HMG box domain binding / otic vesicle development / nephric duct morphogenesis / anatomical structure formation involved in morphogenesis / pro-T cell differentiation / immune system development / interleukin-2 receptor binding / cardiac right ventricle morphogenesis / parathyroid gland development / negative regulation of mammary gland epithelial cell proliferation / ureter maturation / regulation of epithelial cell differentiation / regulation of nephron tubule epithelial cell differentiation / parathyroid hormone secretion / cellular response to interferon-alpha / norepinephrine biosynthetic process / mast cell differentiation / positive regulation of transcription regulatory region DNA binding / positive regulation of signal transduction / mesonephros development / lymphocyte migration / RUNX1 regulates transcription of genes involved in differentiation of HSCs / positive regulation of T-helper 2 cell cytokine production / mesenchymal to epithelial transition / Factors involved in megakaryocyte development and platelet production / ear development / Estrogen-dependent gene expression / histone methyltransferase binding / cell activation / pharyngeal system development / sympathetic nervous system development / positive regulation of interleukin-5 production / cellular response to BMP stimulus / positive regulation of interleukin-13 production / cell fate determination / Ub-specific processing proteases / negative regulation of cell motility / cartilage development / lens development in camera-type eye / aortic valve morphogenesis / embryonic hemopoiesis / T-helper 2 cell differentiation / negative regulation of interleukin-2 production / inner ear morphogenesis / ventricular septum development / positive regulation of T cell differentiation / negative regulation of epithelial to mesenchymal transition / regulation of establishment of cell polarity / regulation of neuron projection development / positive regulation of interleukin-4 production / cellular response to cytokine stimulus / uterus development / E-box binding / negative regulation of type II interferon production / humoral immune response / negative regulation of cell cycle / macrophage differentiation / T cell differentiation / TOR signaling / homeostasis of number of cells / cochlea development / developmental growth / cell fate commitment / canonical Wnt signaling pathway / embryonic organ development / negative regulation of endothelial cell apoptotic process / cis-regulatory region sequence-specific DNA binding / cell maturation / regulation of cytokine production / positive regulation of endothelial cell migration / cellular response to interleukin-4 / regulation of neuron apoptotic process / axon guidance / thymus development / positive regulation of cytokine production / response to gamma radiation / post-embryonic development / erythrocyte differentiation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / positive regulation of cell differentiation / kidney development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of miRNA transcription / response to estrogen / negative regulation of inflammatory response / DNA-binding transcription repressor activity, RNA polymerase II-specific / male gonad development / cellular response to tumor necrosis factor
Similarity search - Function
Transcription factor, GATA-2/3 / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type ...Transcription factor, GATA-2/3 / Transcription factor GATA / GATA-type zinc finger domain. / GATA-type zinc finger domain profile. / zinc finger binding to DNA consensus sequence [AT]GATA[AG] / GATA zinc finger / Zinc finger, GATA-type / Erythroid Transcription Factor GATA-1, subunit A / Erythroid Transcription Factor GATA-1; Chain A / Zinc finger, NHR/GATA-type / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
DNA / DNA (> 10) / Trans-acting T-cell-specific transcription factor GATA-3
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsBates, D.L. / Kim, G.K. / Guo, L. / Chen, L.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structures of multiple GATA zinc fingers bound to DNA reveal new insights into DNA recognition and self-association by GATA.
Authors: Bates, D.L. / Chen, Y. / Kim, G. / Guo, L. / Chen, L.
History
DepositionJun 12, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
X: DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')
Y: DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')
A: Trans-acting T-cell-specific transcription factor GATA-3
B: Trans-acting T-cell-specific transcription factor GATA-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,4836
Polymers26,3524
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5440 Å2
ΔGint-36 kcal/mol
Surface area13140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.882, 30.370, 75.648
Angle α, β, γ (deg.)90.000, 93.820, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: DNA chain DNA (5'-D(*DTP*DTP*DGP*DAP*DTP*DAP*DAP*DAP*DTP*DCP*DAP*DGP*DAP*DGP*DAP*DTP*DAP*DAP*DCP*DC)-3')


Mass: 6150.031 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain DNA (5'-D(*DAP*DAP*DGP*DGP*DTP*DTP*DAP*DTP*DCP*DTP*DCP*DTP*DGP*DAP*DTP*DTP*DTP*DAP*DTP*DC)-3')


Mass: 6113.975 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Trans-acting T-cell-specific transcription factor GATA-3 / GATA-binding factor 3


Mass: 7044.058 Da / Num. of mol.: 2 / Fragment: UNP residues 308-370
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Gata3, Gata-3 / Plasmid: pEt28a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta plyS / References: UniProt: P23772
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.09 %
Crystal growTemperature: 290 K / Method: hanging drop / pH: 6.5
Details: 20 mM Mg(OAc), Cacodylic acid, 30% PEG 4K , pH 6.5, hanging drop, temperature 290K
Components of the solutions
IDNameCrystal-IDSol-ID
1Cacodylic acid11
2Mg(OAc)11
3Cacodylic acid12
4Mg(OAc)12
5PEG 4K12

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.0781 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 12, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0781 Å / Relative weight: 1
ReflectionResolution: 2.7→30 Å / Num. obs: 8491 / % possible obs: 99.9 % / Rmerge(I) obs: 0.085 / Χ2: 1.951 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.7-2.80.4528271.077100
2.8-2.910.3288311.157100
2.91-3.040.2518721.295100
3.04-3.20.1428021.538100
3.2-3.40.1018561.89499.9
3.4-3.660.0878182.161100
3.66-4.030.0748582.414100
4.03-4.610.0688562.628100
4.61-5.80.0678672.801100
5.8-300.0489042.63699.3

-
Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACT3.006data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementResolution: 2.7→25.32 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.755
RfactorNum. reflection
Rfree0.298 864
Rwork0.276 -
obs-8145
Displacement parametersBiso max: 170.54 Å2 / Biso mean: 61.468 Å2 / Biso min: 7.47 Å2
Refinement stepCycle: LAST / Resolution: 2.7→25.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms894 814 2 0 1710

+
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