[English] 日本語
Yorodumi
- PDB-2ls7: High Definition Solution Structure of PED/PEA-15 Death Effector Domain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2ls7
TitleHigh Definition Solution Structure of PED/PEA-15 Death Effector Domain
ComponentsAstrocytic phosphoprotein PEA-15
KeywordsAPOPTOSIS / six helix bundle / death effector domain / death domain superfamily
Function / homology
Function and homology information


RAF-independent MAPK1/3 activation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / RAF/MAP kinase cascade / negative regulation of glucose import / response to morphine / microtubule associated complex / carbohydrate transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / DNA damage checkpoint signaling / protein kinase C binding ...RAF-independent MAPK1/3 activation / positive regulation of extrinsic apoptotic signaling pathway via death domain receptors / RAF/MAP kinase cascade / negative regulation of glucose import / response to morphine / microtubule associated complex / carbohydrate transport / negative regulation of extrinsic apoptotic signaling pathway via death domain receptors / DNA damage checkpoint signaling / protein kinase C binding / intracellular signal transduction / apoptotic process / nucleoplasm / cytosol
Similarity search - Function
Astrocytic phosphoprotein PEA-15, death effector domain / Death effector domain / Death effector domain / Death effector domain (DED) profile. / Death effector domain / Death Domain, Fas / Death Domain, Fas / Death-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Astrocytic phosphoprotein PEA-15
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodSOLUTION NMR / simulated annealing
Model detailsfewest violations, model9
AuthorsTwomey, E.C. / Wei, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: High-definition NMR structure of PED/PEA-15 death effector domain reveals details of key polar side chain interactions.
Authors: Twomey, E.C. / Wei, Y.
History
DepositionApr 20, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Aug 8, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Structure summary
Revision 1.2Jun 14, 2023Group: Data collection / Database references / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model
Revision 1.3May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI
Remark 650HELIX DETERMINATION METHOD: AUTHOR DETERMINED

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Astrocytic phosphoprotein PEA-15


Theoretical massNumber of molelcules
Total (without water)10,7091
Polymers10,7091
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 / 200structures with the lowest energy
RepresentativeModel #1fewest violations

-
Components

#1: Protein Astrocytic phosphoprotein PEA-15 / 15 kDa phosphoprotein enriched in astrocytes


Mass: 10708.981 Da / Num. of mol.: 1 / Fragment: UNP residues 1-90
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Pea15, Pea15a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q62048

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC aliphatic
1313D CBCA(CO)NH
1413D HNCA
1513D HN(CA)CB
1613D HBHA(CO)NH
1713D HNHA
1813D 1H-15N NOESY
1913D (H)CCH-TOCSY
11013D 1H-13C NOESY

-
Sample preparation

DetailsContents: 1 mM [U-100% 13C; U-100% 15N] phosphoprotein enriched in astrocytes 15A, 93% H2O/7% D2O
Solvent system: 93% H2O/7% D2O
SampleConc.: 1 mM / Component: phosphoprotein enriched in astrocytes 15A-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0 / pH: 7 / Pressure: 1 atm / Temperature: 298 K

-
NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR softwareName: X-PLOR NIH / Version: 2.29 / Developer: Schwieters, Kuszewski, Tjandra and Clore / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 1985 / NOE intraresidue total count: 341 / NOE long range total count: 483 / NOE medium range total count: 611 / NOE sequential total count: 464
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / 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