[English] 日本語
Yorodumi
- PDB-1gnf: SOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGER OF MURINE GATA-1... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gnf
TitleSOLUTION STRUCTURE OF THE N-TERMINAL ZINC FINGER OF MURINE GATA-1, NMR, 25 STRUCTURES
ComponentsTRANSCRIPTION FACTOR GATA-1
KeywordsTRANSCRIPTION REGULATION / ZINC FINGER
Function / homology
Function and homology information


regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / myeloid cell apoptotic process / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of glycoprotein biosynthetic process / 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 / negative regulation of bone mineralization / Factors involved in megakaryocyte development and platelet production / cellular response to follicle-stimulating hormone stimulus / positive regulation of mast cell degranulation / negative regulation of myeloid cell apoptotic process / myeloid cell differentiation / C2H2 zinc finger domain binding / embryonic hemopoiesis / platelet formation / bone mineralization / positive regulation of osteoblast proliferation / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / cell fate commitment / cis-regulatory region sequence-specific DNA binding / animal organ regeneration / erythrocyte development / cellular response to cAMP / homeostasis of number of cells within a tissue / transcription repressor complex / positive regulation of erythrocyte differentiation / erythrocyte differentiation / transcription coregulator binding / protein-DNA complex / chromatin DNA binding / platelet aggregation / transcription coactivator binding / positive regulation of peptidyl-tyrosine phosphorylation / p53 binding / cell-cell signaling / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / sequence-specific DNA binding / transcription by RNA polymerase II / cell population proliferation / 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 / chromatin binding / 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
Similarity search - Function
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
Erythroid transcription factor
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsKowalski, K. / Czolij, R. / King, G.F. / Crossley, M. / Mackay, J.P.
CitationJournal: J.Biomol.NMR / Year: 1999
Title: The solution structure of the N-terminal zinc finger of GATA-1 reveals a specific binding face for the transcriptional co-factor FOG.
Authors: Kowalski, K. / Czolij, R. / King, G.F. / Crossley, M. / Mackay, J.P.
History
DepositionOct 12, 1998Processing site: BNL
Revision 1.0Jun 8, 1999Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4May 1, 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_ref_seq_dif / 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_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: TRANSCRIPTION FACTOR GATA-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,2652
Polymers5,2001
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)25 / 1000LOWEST RESIDUAL RESTRAINT VIOLATIONS
Representative

-
Components

#1: Protein/peptide TRANSCRIPTION FACTOR GATA-1


Mass: 5199.939 Da / Num. of mol.: 1 / Fragment: N-TERMINAL ZINC FINGER
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line: BL21 / Plasmid: PGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P17679
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111TOCSY
121DQFCOSY
131NOESY
141ECOSY
151HSQC
161TOCSY-HSQC
171NOESY-HSQC
181J-MODULATED HMQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING HOMONUCLEAR 1H, AND HETERONUCLEAR 1H/15N NMR SPECTROSCOPY

-
Sample preparation

DetailsContents: 95% H2O:5% D2O
Sample conditionspH: 5.4 / Pressure: 1 atm / Temperature: 288 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMX600BrukerAMX6006001
Bruker DRX500BrukerDRX5006002

-
Processing

Software
NameVersionClassification
X-PLOR3.843model building
X-PLOR3.843refinement
X-PLOR3.843phasing
NMR software
NameVersionDeveloperClassification
X-PLOR3.843BRUNGERrefinement
DIANA2.12structure solution
X-PLOR3.843structure solution
RefinementMethod: DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOWEST RESIDUAL RESTRAINT VIOLATIONS
Conformers calculated total number: 1000 / Conformers submitted total number: 25

+
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