[English] 日本語
Yorodumi
- PDB-2kmd: Ras signaling requires dynamic properties of Ets1 for phosphoryla... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2kmd
TitleRas signaling requires dynamic properties of Ets1 for phosphorylation-enhanced binding to co-activator CBP
ComponentsProtein C-ets-1
KeywordsTRANSCRIPTION / PROTEIN BINDING / PNT DOMAIN / SAM DOMAIN / ETS-1 / MAPK PHOSPHORYLATION / PHOSPHOPROTEIN / PROTO-ONCOGENE / TRANSCRIPTION REGULATION / CONFORMATIONAL DYNAMICS
Function / homology
Function and homology information


Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding ...Oncogene Induced Senescence / regulation of extracellular matrix disassembly / histone acetyltransferase binding / immune system process / regulation of angiogenesis / positive regulation of endothelial cell migration / positive regulation of erythrocyte differentiation / negative regulation of inflammatory response / positive regulation of angiogenesis / sequence-specific double-stranded DNA binding / DNA-binding transcription factor binding / sequence-specific DNA binding / transcription regulator complex / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / positive regulation of cell migration / DNA-binding transcription factor activity / positive regulation of cell population proliferation / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / cytoplasm
Similarity search - Function
Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. ...Protein C-ets-1, pointed domain / Transforming protein C-ets / Ets1, N-terminal flanking region of Ets domain / Ets1 N-terminal flanking region of Ets domain / SAM / Pointed domain / Pointed domain / Sterile alpha motif (SAM)/Pointed domain / Pointed (PNT) domain profile. / Transcription Factor, Ets-1 / Ets-domain signature 1. / Ets-domain signature 2. / Ets domain / ETS family / Ets-domain / Ets-domain profile. / erythroblast transformation specific domain / Sterile alpha motif/pointed domain superfamily / DNA polymerase; domain 1 / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
AuthorsNelson, M.L. / Kang, H. / Lee, G.M. / Blaszczak, A.G. / Lau, D.K.W. / McIntosh, L.P. / Graves, B.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2010
Title: Ras signaling requires dynamic properties of Ets1 for phosphorylation-enhanced binding to coactivator CBP.
Authors: Nelson, M.L. / Kang, H.S. / Lee, G.M. / Blaszczak, A.G. / Lau, D.K. / McIntosh, L.P. / Graves, B.J.
History
DepositionJul 27, 2009Deposition site: BMRB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Oct 9, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_nmr_software / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Protein C-ets-1


Theoretical massNumber of molelcules
Total (without water)13,0101
Polymers13,0101
Non-polymers00
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 / 500structures with the lowest energy
RepresentativeModel #1lowest energy

-
Components

#1: Protein Protein C-ets-1 / p54


Mass: 13009.754 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ets1, Ets-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P27577
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HN(CA)CB
1413D (H)CCH-TOCSY
1513D 1H-15N NOESY
1613D 1H-15N TOCSY
1713D 1H-13C NOESY
1813D CBCA(CO)NH
191IPAP
1101CLEANEX
1111T1 T2 HNNOE
1121HN(CO)CA HACA

-
Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] 2P-ETS1PNT, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 1 mM / Component: 2P-ETS1PNT / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 20 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 600 MHz

-
Processing

NMR software
NameDeveloperClassification
CYANAGuntert, P. et al.structure solution
SCULPTOR(SCULPTOR)-Martin Blackledgerefinement
SparkyGoddard, T. et al.chemical shift assignment
NMRDrawDelaglio, F. et al.processing
MOLMOLKoradi, R. et al.data analysis
ProcheckNMRLaskowski, R. et al.data analysis
VNMRVariancollection
TALOSCornilescu, G. et al.data analysis
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 500 / 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