[English] 日本語
Yorodumi
- PDB-4hc9: DNA binding by GATA transcription factor-complex 3 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4hc9
TitleDNA binding by GATA transcription factor-complex 3
Components
  • DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
  • DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
  • Trans-acting T-cell-specific transcription factor GATA-3
KeywordsTranscription/DNA / zinc finger / GATA transcription factor / DNA bridging / Transcription-DNA complex
Function / homology
Function and homology information


nephric duct formation / negative regulation of cell proliferation involved in mesonephros development / regulation of cellular response to X-ray / negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation / negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of ureteric bud formation / : ...nephric duct formation / negative regulation of cell proliferation involved in mesonephros development / regulation of cellular response to X-ray / negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation / negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation / ureter morphogenesis / thymic T cell selection / ureteric bud formation / positive regulation of ureteric bud formation / : / HMG box domain binding / positive regulation of thyroid hormone generation / otic vesicle development / anatomical structure formation involved in morphogenesis / pro-T cell differentiation / negative regulation of mammary gland epithelial cell proliferation / nephric duct morphogenesis / interleukin-2 receptor binding / norepinephrine biosynthetic process / cardiac right ventricle morphogenesis / cellular response to interferon-alpha / immune system development / parathyroid gland development / ureter maturation / mesenchymal to epithelial transition / mast cell differentiation / parathyroid hormone secretion / regulation of nephron tubule epithelial cell differentiation / regulation of epithelial cell differentiation / positive regulation of signal transduction / lymphocyte migration / mesonephros development / Formation of the nephric duct / positive regulation of T-helper 2 cell cytokine production / regulation of T-helper cell differentiation / ear development / positive regulation of interleukin-13 production / positive regulation of interleukin-5 production / pharyngeal system development / sympathetic nervous system development / negative regulation of cell motility / cellular response to BMP stimulus / cell fate determination / positive regulation of transcription regulatory region DNA binding / negative regulation of epithelial to mesenchymal transition / T-helper 2 cell differentiation / aortic valve morphogenesis / cartilage development / regulation of establishment of cell polarity / lens development in camera-type eye / positive regulation of T cell differentiation / embryonic hemopoiesis / ventricular septum development / negative regulation of interleukin-2 production / regulation of neuron projection development / inner ear morphogenesis / positive regulation of interleukin-4 production / E-box binding / uterus development / humoral immune response / macrophage differentiation / negative regulation of type II interferon production / negative regulation of cell cycle / T cell differentiation / developmental growth / TOR signaling / anatomical structure morphogenesis / canonical Wnt signaling pathway / cell fate commitment / embryonic organ development / cellular response to interleukin-4 / cis-regulatory region sequence-specific DNA binding / negative regulation of endothelial cell apoptotic process / regulation of neuron apoptotic process / cell maturation / regulation of cytokine production / positive regulation of endothelial cell migration / erythrocyte differentiation / phosphatidylinositol 3-kinase/protein kinase B signal transduction / post-embryonic development / thymus development / kidney development / axon guidance / neuron migration / response to virus / defense response / transcription coactivator binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / negative regulation of inflammatory response / response to estrogen / male gonad development / sequence-specific double-stranded DNA binding / cellular response to tumor necrosis factor / RUNX1 regulates transcription of genes involved in differentiation of HSCs / T cell receptor signaling pathway / Factors involved in megakaryocyte development and platelet production / DNA-binding transcription activator activity, RNA polymerase II-specific / Interleukin-4 and Interleukin-13 signaling / Estrogen-dependent gene expression
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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsChen, Y. / Bates, D.L. / Dey, R. / Chen, L.
CitationJournal: Cell Rep / Year: 2012
Title: DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation.
Authors: Chen, Y. / Bates, D.L. / Dey, R. / Chen, P.H. / Machado, A.C. / Laird-Offringa, I.A. / Rohs, R. / Chen, L.
History
DepositionSep 28, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 5, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 2, 2013Group: Database references
Revision 1.2Dec 17, 2014Group: Data collection
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details / _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
A: Trans-acting T-cell-specific transcription factor GATA-3
Y: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
Z: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2905
Polymers25,1593
Non-polymers1312
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2840 Å2
ΔGint-23 kcal/mol
Surface area14610 Å2
MethodPISA
2
A: Trans-acting T-cell-specific transcription factor GATA-3
hetero molecules

Y: DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')
Z: DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')


Theoretical massNumber of molelcules
Total (without water)25,2905
Polymers25,1593
Non-polymers1312
Water543
TypeNameSymmetry operationNumber
crystal symmetry operation4_546-x+1/2,y-1/2,-z+11
identity operation1_555x,y,z1
Buried area3780 Å2
ΔGint-26 kcal/mol
Surface area13670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.118, 30.352, 72.475
Angle α, β, γ (deg.)90.000, 98.590, 90.000
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein Trans-acting T-cell-specific transcription factor GATA-3 / GATA-binding factor 3


Mass: 12893.872 Da / Num. of mol.: 1 / Fragment: UNP residues 260 -365
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GATA3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P23771
#2: DNA chain DNA (5'-D(*TP*TP*CP*CP*TP*AP*AP*AP*TP*CP*AP*GP*AP*GP*AP*TP*AP*AP*CP*C)-3')


Mass: 6085.982 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#3: DNA chain DNA (5'-D(*AP*AP*GP*GP*TP*TP*AP*TP*CP*TP*CP*TP*GP*AP*TP*TP*TP*AP*GP*G)-3')


Mass: 6179.013 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: This sequence occurs naturally in humans.
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growMethod: hanging drop / Details: hanging drop

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. obs: 31114

-
Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→50 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 3861
RfactorNum. reflection% reflection
Rfree0.2162 3094 8.5 %
Rwork0.1811 --
obs-31114 85.4 %
Solvent computationBsol: 52.422 Å2
Displacement parametersBiso max: 128.41 Å2 / Biso mean: 31.9677 Å2 / Biso min: 9.73 Å2
Baniso -1Baniso -2Baniso -3
1-2.355 Å20 Å2-0.062 Å2
2---2.822 Å20 Å2
3---0.467 Å2
Refinement stepCycle: LAST / Resolution: 1.6→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms821 814 2 336 1973
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.4841.5
X-RAY DIFFRACTIONc_scbond_it1.7592
X-RAY DIFFRACTIONc_mcangle_it2.4612
X-RAY DIFFRACTIONc_scangle_it2.6552.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param
X-RAY DIFFRACTION4CNS_TOPPAR:water_rep.param

+
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://pdbjlvh1.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