[English] 日本語
Yorodumi
- PDB-2bn6: P-Element Somatic Inhibitor Protein -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2bn6
TitleP-Element Somatic Inhibitor Protein
ComponentsPSI
KeywordsNUCLEAR PROTEIN / SPLICING / PROTEIN-PROTEIN INTERACTION / PROLINE-RICH PEPTIDE
Function / homology
Function and homology information


regulation of mRNA splicing, via spliceosome / regulation of alternative mRNA splicing, via spliceosome / negative regulation of mRNA splicing, via spliceosome / mRNA processing / spermatogenesis / mRNA binding / regulation of DNA-templated transcription / nucleus
Similarity search - Function
Far upstream element-binding protein, C-terminal / Domain of unknown function (DUF1897) / KH domain / K Homology domain, type 1 / Type-1 KH domain profile. / K Homology domain, type 1 superfamily / K Homology domain / K homology RNA-binding domain
Similarity search - Domain/homology
Biological speciesDROSOPHILA MELANOGASTER (fruit fly)
MethodSOLUTION NMR / SIMULATED ANNEAING
AuthorsIgnjatovic, T. / Yang, J.C. / Butler, P.J.G. / Neuhaus, D. / Nagai, K.
CitationJournal: J.Mol.Biol. / Year: 2005
Title: Structural Basis of the Interaction between P-Element Somatic Inhibitor and U1-70K Essential for the Alternative Splicing of P-Element Transposase.
Authors: Ignjatovic, T. / Yang, J.C. / Butler, J. / Neuhaus, D. / Nagai, K.
History
DepositionMar 21, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 6, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PSI


Theoretical massNumber of molelcules
Total (without water)3,7961
Polymers3,7961
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)29 / 50LOW NOE ENERGY
RepresentativeModel #1

-
Components

#1: Protein/peptide PSI / P-ELEMENT SOMATIC INHIBITOR


Mass: 3796.136 Da / Num. of mol.: 1 / Fragment: B BOX, RESIDUES 651-683
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DROSOPHILA MELANOGASTER (fruit fly) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q7JPS0
Sequence detailsRESIDUES 651-683 ONLY

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111NOESY
121TOCSY
1312D 1H-15N HSQC
1413D 1H-15N NOESY-HSQC
1513D 1H-15N TOCSY-HSQC
NMR detailsText: THE STRUCTURE WAS DETERMINED USING 15N LABELLED PROTEIN.

-
Sample preparation

DetailsContents: 93% H2O, 7% D2O
Sample conditionsIonic strength: 100MM NACL, 10MM SODIUM PHOSPHATE / pH: 6.5 / Pressure: 1.0 atm / Temperature: 290.0 K

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAvance8001
Bruker DRXBrukerDRX5002

-
Processing

NMR software
NameDeveloperClassification
CNSBRUNGER,ADAMS,CLORE,DELANO,GROS, GROSSE- KUNSTLEVE,JIANG,KUSZEWSKI,NILGES, PANNU,READ, RICE,SIMONSON,WARRENrefinement
CNSstructure solution
RefinementMethod: SIMULATED ANNEAING / Software ordinal: 1
Details: REFINEMENT DETAILS CAN BE FOUND IN THE JRNL CITATION ABOVE
NMR ensembleConformer selection criteria: LOW NOE ENERGY / Conformers calculated total number: 50 / Conformers submitted total number: 29

+
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