[English] 日本語
Yorodumi
- PDB-1srk: Solution structure of the third zinc finger domain of FOG-1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1srk
TitleSolution structure of the third zinc finger domain of FOG-1
ComponentsZinc finger protein ZFPM1
KeywordsTRANSCRIPTION / classical zinc finger
Function / homology
Function and homology information


tricuspid valve formation / negative regulation of mast cell differentiation / regulation of definitive erythrocyte differentiation / regulation of chemokine production / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation / megakaryocyte differentiation ...tricuspid valve formation / negative regulation of mast cell differentiation / regulation of definitive erythrocyte differentiation / regulation of chemokine production / definitive erythrocyte differentiation / negative regulation of interleukin-4 production / mitral valve formation / atrial septum morphogenesis / primitive erythrocyte differentiation / megakaryocyte differentiation / granulocyte differentiation / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Factors involved in megakaryocyte development and platelet production / cardiac muscle tissue morphogenesis / atrioventricular valve morphogenesis / embryonic hemopoiesis / platelet formation / megakaryocyte development / ventricular septum morphogenesis / outflow tract morphogenesis / homeostasis of number of cells / transcription repressor complex / erythrocyte differentiation / negative regulation of protein binding / positive regulation of type II interferon production / transcription corepressor activity / heart development / RNA polymerase II-specific DNA-binding transcription factor binding / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / metal ion binding
Similarity search - Function
: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Zinc-finger of C2H2 type / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily ...: / Zinc finger protein ZFPM1-like, PR domain / Zinc finger CCHC FOG-type / FOG family / Zinc finger CCHC FOG-type profile. / Zinc-finger of C2H2 type / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
Zinc finger protein ZFPM1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing, molecular dynamics, torsion angle dynamics
AuthorsSimpson, R.J.Y. / Lee, S.H.Y. / Bartle, N. / Matthews, J.M. / Mackay, J.P. / Crossley, M.
CitationJournal: J.Biol.Chem. / Year: 2004
Title: A Classic Zinc Finger from Friend of GATA Mediates an Interaction with the Coiled-coil of Transforming Acidic Coiled-coil 3.
Authors: Simpson, R.J.Y. / Lee, S.H.Y. / Bartle, N. / Sum, E.Y. / Visvader, J.E. / Matthews, J.M. / Mackay, J.P. / Crossley, M.
History
DepositionMar 22, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 21, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 27, 2021Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / 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_nmr_software.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Zinc finger protein ZFPM1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,8802
Polymers3,8141
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 1000structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein/peptide Zinc finger protein ZFPM1 / Zinc finger protein multitype 1 / Friend of GATA protein 1 / Friend of GATA-1 / FOG-1


Mass: 3814.467 Da / Num. of mol.: 1 / Fragment: residues 328-360 / Mutation: E330K, L336R, E349A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: ZFPM1, FOG1, FOG / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: O35615
#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
1112D NOESY
1212D TOCSY
131DQF-COSY
242HNHA
NMR detailsText: Structure was determined using standard 2D homonuclear NMR spectroscopy

-
Sample preparation

Details
Solution-IDContentsSolvent system
10.27 mM FOG-F3, 2mM TCEP, 1 mM ZnSO4, 95% H2O, 5% D2O95% H2O/5% D2O
20.245 mM 15N-FOG-F3, 2mM TCEP, 1 mM ZnSO4, 95% H2O, 5% D2O95% H2O/5% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
10 mM 5.6ambient 275 K
20 mM 5.6ambient 275 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
XwinNMR2.6Brukerprocessing
XEASY1.3.13Bartels et aldata analysis
DYANA1.5Guntert et alrefinement
ARIA1.2Linge et alstructure solution
RefinementMethod: simulated annealing, molecular dynamics, torsion angle dynamics
Software ordinal: 1
Details: final structures were based on 859 unambiguous NOE-derived distance constraints, 20 ambiguous constraints and 31 dihedral angle restraints
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 1000 / 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://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