[English] 日本語
Yorodumi
- PDB-1y0j: Zinc fingers as protein recognition motifs: structural basis for ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y0j
TitleZinc fingers as protein recognition motifs: structural basis for the GATA-1/Friend of GATA interaction
Components
  • Erythroid transcription factor
  • Zinc-finger protein ush
KeywordsDNA BINDING PROTEIN / zinc finger / GATA-1 / FOG / protein-protein complex
Function / homology
Function and homology information


lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / germ-band shortening ...lymph gland plasmatocyte differentiation / lymph gland crystal cell differentiation / negative regulation of hemocyte differentiation / amnioserosa maintenance / positive regulation of antibacterial peptide biosynthetic process / regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / germ-band shortening / larval lymph gland hemopoiesis / Factors involved in megakaryocyte development and platelet production / lymph gland development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / compound eye development / regulation of glycoprotein biosynthetic process / chaeta development / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Sertoli cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / dendritic cell differentiation / cellular response to follicle-stimulating hormone stimulus / negative regulation of bone mineralization / Factors involved in megakaryocyte development and platelet production / negative regulation of myeloid cell apoptotic process / positive regulation of mast cell degranulation / myeloid cell differentiation / C2H2 zinc finger domain binding / embryonic hemopoiesis / platelet formation / DNA-binding transcription repressor activity / bone mineralization / positive regulation of osteoblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell fate commitment / animal organ regeneration / cis-regulatory region sequence-specific DNA binding / erythrocyte development / cellular response to cAMP / homeostasis of number of cells within a tissue / transcription repressor complex / negative regulation of insulin receptor signaling pathway / erythrocyte differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / protein-DNA complex / chromatin DNA binding / transcription coactivator binding / platelet aggregation / positive regulation of peptidyl-tyrosine phosphorylation / p53 binding / cell-cell signaling / heart development / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / sequence-specific DNA binding / transcription by RNA polymerase II / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / negative regulation of DNA-templated transcription / chromatin binding / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / 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 / Zinc-finger of C2H2 type ...Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / 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 / Zinc-finger of C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2-type / Zinc finger, NHR/GATA-type
Similarity search - Domain/homology
Erythroid transcription factor / Zinc finger protein ush
Similarity search - Component
Biological speciesMus musculus (house mouse)
Drosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing, molecular dynamics torsion angle dynamics
AuthorsLiew, C.K. / Simpson, R.J.Y. / Kwan, A.H.Y. / Crofts, L.A. / Loughlin, F.E. / Matthews, J.M. / Crossley, M. / Mackay, J.P.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: Zinc fingers as protein recognition motifs: Structural basis for the GATA-1/Friend of GATA interaction
Authors: Liew, C.K. / Simpson, R.J.Y. / Kwan, A.H.Y. / Crofts, L.A. / Loughlin, F.E. / Matthews, J.M. / Crossley, M. / Mackay, J.P.
History
DepositionNov 15, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 25, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / 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_nmr_software.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Erythroid transcription factor
B: Zinc-finger protein ush
hetero molecules


Theoretical massNumber of molelcules
Total (without water)9,2924
Polymers9,1622
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Erythroid transcription factor / GATA-1 / Eryf1 / GF-1 / NF-E1


Mass: 5199.939 Da / Num. of mol.: 1 / Fragment: GNF
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: gata-1 / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P17679
#2: Protein/peptide Zinc-finger protein ush / U-SHAPED TRANSCRIPTION FACTOR / U-shaped protein


Mass: 3961.636 Da / Num. of mol.: 1 / Fragment: USF1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: u-shaped / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9VPQ6
#3: Chemical ChemComp-ZN / ZINC ION


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

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HNCO
121HNCA
133HNCA
143HN(CO)CA
152HNCA
162CBCA(CO)NH
17215N, 13C double decoupled NOESY
182(H)CCH-TOCSY
19415N, 13C double half-filtered NOESY
1104HN(CA)CB
NMR detailsText: Other commonly used standard triple-resonance NMR experiments were also recorded.

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM GNF U-15N,13C; 2mM tris-carboxyethylphosphine (TCEP); 1mM zinc sulphate; 20mM Sodium Acetate95% H2O/5% D2O
20.5mM GNF U-15N,13C; 0.6mM USF1; 2mM tris-carboxyethylphosphine (TCEP); 1mM zinc sulphate; 20mM Sodium Acetate95% H2O/5% D2O
30.5mM USF1 U-15N,13C; 2mM tris-carboxyethylphosphine (TCEP); 1mM zinc sulphate; 20mM Sodium Acetate95% H2O/5% D2O
40.5mM GNF; 0.6mM USF1 U-15N,13C; 2mM tris-carboxyethylphosphine (TCEP); 1mM zinc sulphate; 20mM Sodium Acetate95% H2O/5% D2O
Sample conditionspH: 5.5 / Pressure: ambient / Temperature: 280 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DRX / Manufacturer: Bruker / Model: DRX / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.5Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
ARIA1.2Linge et alstructure solution
HADDOCK1Donminguez et alstructure solution
HADDOCK1Donminguez et alrefinement
RefinementMethod: simulated annealing, molecular dynamics torsion angle dynamics
Software ordinal: 1
Details: Standard triple-resonance NMR spectroscopy was first used to determine the preliminary structure of the complex. Since the backbone folds of both GNF and USF1 did not appear to be ...Details: Standard triple-resonance NMR spectroscopy was first used to determine the preliminary structure of the complex. Since the backbone folds of both GNF and USF1 did not appear to be substantially altered to those of the proteins in isolation, the computer program Haddock was used to dock the two partner proteins using intermolecular NOEs obtained from double half-filtered NOESY experiments, and ambiguous restraints derived from mutagenesis and NMR titration experiments.
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

+
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