[English] 日本語
Yorodumi
- PDB-2l6y: haddock model of GATA1NF:Lmo2LIM2-Ldb1LID -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2l6y
Titlehaddock model of GATA1NF:Lmo2LIM2-Ldb1LID
Components
  • Erythroid transcription factor
  • LIM domain only 2, linker, LIM domain-binding protein 1
KeywordsTranscription regulation/ONCOPROTEIN / gata-1 / ldb1 / lmo2 / fog-1 / Transcription regulation-ONCOPROTEIN complex
Function / homology
Function and homology information


regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / regulation of glycoprotein biosynthetic process / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation ...regulation of primitive erythrocyte differentiation / basophil differentiation / eosinophil fate commitment / regulation of definitive erythrocyte differentiation / regulation of kinase activity / cellular component assembly / negative regulation of erythrocyte differentiation / regulation of glycoprotein biosynthetic process / positive regulation of hemoglobin biosynthetic process / cerebellar Purkinje cell differentiation / epithelial structure maintenance / myeloid cell apoptotic process / head development / primitive erythrocyte differentiation / megakaryocyte differentiation / osteoblast proliferation / cell development / beta-catenin-TCF complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Sertoli cell development / RUNX1 regulates transcription of genes involved in differentiation of HSCs / transcription-dependent tethering of RNA polymerase II gene DNA at nuclear periphery / LIM domain binding / 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 / gastrulation with mouth forming second / anterior/posterior axis specification / embryonic hemopoiesis / platelet formation / regulation of focal adhesion assembly / cell leading edge / bone mineralization / positive regulation of osteoblast proliferation / somatic stem cell population maintenance / positive regulation of cell adhesion / negative regulation of extrinsic apoptotic signaling pathway in absence of ligand / hair follicle development / 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 / regulation of cell migration / transcription repressor complex / cerebellum development / erythrocyte differentiation / positive regulation of erythrocyte differentiation / transcription coregulator binding / protein-DNA complex / positive regulation of transcription elongation by RNA polymerase II / neuron differentiation / chromatin DNA binding / Wnt signaling pathway / transcription coactivator binding / platelet aggregation / RNA polymerase II transcription regulator complex / : / positive regulation of peptidyl-tyrosine phosphorylation / p53 binding / cell-cell signaling / nervous system development / positive regulation of cytosolic calcium ion concentration / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / DNA-binding transcription factor binding / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / cell population proliferation / transcription regulator complex / sequence-specific DNA binding / transcription by RNA polymerase II / transcription coactivator activity / cell adhesion / 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 / chromatin / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / metal ion binding
Similarity search - Function
LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain 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 ...LIM-domain binding protein/SEUSS / LIM interaction domain / LIM-domain binding protein / LIM interaction domain (LID) / LIM interaction domain (LID) domain 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 / Cysteine Rich Protein / Cysteine Rich Protein / LIM zinc-binding domain signature. / LIM domain / Zinc-binding domain present in Lin-11, Isl-1, Mec-3. / Zinc finger, LIM-type / LIM domain profile. / Ribbon / Zinc finger, NHR/GATA-type / Mainly Beta
Similarity search - Domain/homology
Erythroid transcription factor / Rhombotin-2 / LIM domain-binding protein 1 / Rhombotin-2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailslowest energy, model 1
AuthorsWilkinson-White, L. / Gamsjaeger, R. / Dastmalchi, S. / Wienert, B. / Stokes, P.H. / Crossley, M. / Mackay, J.P. / Matthews, J.M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Structural basis of simultaneous recruitment of the transcriptional regulators LMO2 and FOG1/ZFPM1 by the transcription factor GATA1
Authors: Wilkinson-White, L. / Gamsjaeger, R. / Dastmalchi, S. / Wienert, B. / Stokes, P.H. / Crossley, M. / Mackay, J.P. / Matthews, J.M.
History
DepositionDec 1, 2010Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 31, 2011Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2011Group: Database references / Structure summary
Revision 1.2May 1, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq / 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_spectrometer.model / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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_asym_id / _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_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _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: Erythroid transcription factor
B: LIM domain only 2, linker, LIM domain-binding protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,1785
Polymers14,9822
Non-polymers1963
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 10all calculated structures submitted
RepresentativeModel #1lowest energy

-
Components

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


Mass: 4417.993 Da / Num. of mol.: 1 / Fragment: GATA-type 1 domain, residues 200-238
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli) / References: UniProt: P17679
#2: Protein LIM domain only 2, linker, LIM domain-binding protein 1 / LMO2 / LDB1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor ...LMO2 / LDB1 / Carboxyl-terminal LIM domain-binding protein 2 / CLIM-2 / LIM domain-binding factor CLIM2 / mLdb1 / Nuclear LIM interactor


Mass: 10564.112 Da / Num. of mol.: 1
Fragment: residues 84-155; LIM-binding domain (LID), UNP residues 336-348
Mutation: C130S
Source method: isolated from a genetically manipulated source
Details: including a flexible linker region, GGSGGSGGSGG / Source: (gene. exp.) Mus musculus (house mouse) / Production host: Escherichia coli (E. coli)
References: UniProt: Q544Z2, UniProt: P70662, UniProt: P25801*PLUS
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

-
Sample preparation

DetailsContents: 1mM [U-15N] GATA1NF; 90% H2O/10% D2O / Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: entity_1-1 / Isotopic labeling: [U-15N]
Sample conditionsIonic strength: 0.12 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

-
Processing

NMR softwareName: CNS / Developer: Brunger, Adams, Clore, Gros, Nilges and Read / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1 / Details: haddock (2.1) model
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: all calculated structures submitted
Conformers calculated total number: 10 / Conformers submitted total number: 10 / Representative conformer: 1

+
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