[English] 日本語
Yorodumi
- PDB-2vxe: SOLUTION STRUCTURE OF THE LSM DOMAIN OF DROSOPHILA MELANOGASTER T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2vxe
TitleSOLUTION STRUCTURE OF THE LSM DOMAIN OF DROSOPHILA MELANOGASTER TRAL (TRAILER HITCH)
ComponentsCG10686-PA
KeywordsTRANSCRIPTION / EDC3 / CAR-1 / P-BODIES / DECAPPING / MRNA DECAY / LSM PROTEINS / TRANSLATIONAL REPRESSION
Function / homology
Function and homology information


fusome / DEAD/H-box RNA helicase binding / positive regulation of determination of dorsal identity / positive regulation of protein exit from endoplasmic reticulum / P-body assembly / endoplasmic reticulum organization / P granule / stress granule assembly / spliceosomal complex / P-body ...fusome / DEAD/H-box RNA helicase binding / positive regulation of determination of dorsal identity / positive regulation of protein exit from endoplasmic reticulum / P-body assembly / endoplasmic reticulum organization / P granule / stress granule assembly / spliceosomal complex / P-body / microtubule cytoskeleton organization / actin cytoskeleton organization / mRNA binding / cytosol
Similarity search - Function
FFD box / TFG box / FFD box profile. / TFG box profile. / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain ...FFD box / TFG box / FFD box profile. / TFG box profile. / Lsm14-like, N-terminal / Scd6-like Sm domain / Scd6-like Sm domain / FDF domain / FDF domain / DFDF domain / DFDF domain profile. / FDF / SH3 type barrels. - #100 / : / Sm domain profile. / LSM domain superfamily / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / XPLOR
AuthorsTritschler, F. / Coles, M. / Truffault, V.
CitationJournal: Mol.Cell.Biol. / Year: 2008
Title: Similar Modes of Interaction Enable Trailer Hitch and Edc3 to Associate with Dcp1 and Me31B in Distinct Protein Complexes.
Authors: Tritschler, F. / Eulalio, A. / Helms, S. / Schmidt, S. / Coles, M. / Weichenrieder, O. / Izaurralde, E. / Truffault, V.
History
DepositionJul 3, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Source and taxonomy / Version format compliance
Revision 1.2May 15, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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_mr / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: CG10686-PA


Theoretical massNumber of molelcules
Total (without water)9,7771
Polymers9,7771
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)24 / 50MINIMUM ENERGY
RepresentativeModel #1

-
Components

#1: Protein CG10686-PA / GH08269P / TRAL-TRAILER HITCH


Mass: 9777.012 Da / Num. of mol.: 1 / Fragment: LSM DOMAIN, RESIDUES 1-84
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Cell line: S2 CELLS / Plasmid: PETM60 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): K12 / References: UniProt: Q9VTZ0

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111HN(CA)CO
121HNCO
131HN(CA)CB
141CBCA(CO)NH
151HNHA
161HNHB
171CCH- COSY
181CCH-TOCSY
191HNH-NOESY
1101NNH-NOESY
1111CNH-NOESY
1121HCH- NOESY
NMR detailsText: THE STRUCTURE WAS DETERMINED USING TRIPLE-RESONANCE NMR SPECTROSCOPY ON 15N, AND 13C, 15N-LABELED DROSOPHILA MELANOGASTER TRAL LSM DOMAIN

-
Sample preparation

DetailsContents: 1X PBS, 1 MM DTT, PH7.2, 10% D2O
Sample conditionsIonic strength: 150 mM / pH: 7.2 / Pressure: 1.0 atm / Temperature: 298.0 K

-
NMR measurement

NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 900 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
X-PLOR2.9.4BRUNGERrefinement
Sparkystructure solution
RefinementMethod: XPLOR / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN THE PUBLICATION
NMR ensembleConformer selection criteria: MINIMUM ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 24

+
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