[English] 日本語
Yorodumi
- PDB-1qtu: SOLUTION STRUCTURE OF THE ONCOPROTEIN P13MTCP1 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qtu
TitleSOLUTION STRUCTURE OF THE ONCOPROTEIN P13MTCP1
ComponentsPROTEIN (PRODUCT OF THE MTCP1 ONCOGENE)
KeywordsGENE REGULATION / BETA BARREL
Function / homology
Function and homology information


protein serine/threonine kinase activator activity / intracellular signal transduction / protein kinase binding
Similarity search - Function
Proto-oncogene - Oncogene Product P14tcl1 / TCL1/MTCP1 / TCL1/MTCP1 / TCL1/MTCP1 superfamily / TCL1/MTCP1 family / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
Model type detailsminimized average
AuthorsGuignard, L. / Padilla, A. / Mispelter, J. / Yang, Y.-S. / Stern, M.-H. / Lhoste, J.-M. / Roumestand, C.
Citation
Journal: J.Biomol.NMR / Year: 2000
Title: Backbone dynamics and solution structure refinement of the 15N-labeled human oncogenic protein p13MTCP1: comparison with X-ray data.
Authors: Guignard, L. / Padilla, A. / Mispelter, J. / Yang, Y.S. / Stern, M.H. / Lhoste, J.M. / Roumestand, C.
#1: Journal: J.Biomol.NMR / Year: 1998
Title: Solution structure of the recombinant human oncoprotein p13MTCP1
Authors: Yang, Y.-S. / Guignard, L. / Padilla, A. / Hoh, F. / Strub, M.-P.
History
DepositionJun 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _audit_author.name / _citation_author.name
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (PRODUCT OF THE MTCP1 ONCOGENE)


Theoretical massNumber of molelcules
Total (without water)13,6801
Polymers13,6801
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / -
Representativeminimized average structure

-
Components

#1: Protein PROTEIN (PRODUCT OF THE MTCP1 ONCOGENE)


Mass: 13680.420 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell: T-CELLS / Cell (production host): BL21 / Production host: Escherichia coli (E. coli) / References: UniProt: P56278

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
1212D NOESY
131DQF-COSY

-
Sample preparation

DetailsContents: 2mM p13MTCP1 U-15N; 20mM phosphate buffer NA;90% H2O, 10% D2O
Solvent system: 90% H2O/10% D2O
Sample conditionspH: 6.5 / Pressure: ambient / Temperature: 303 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AMXBrukerAMX6001
Bruker DMXBrukerDMX8002
Bruker AMXBrukerAMX4003

-
Processing

NMR softwareName: Amber / Version: 4.1 / Developer: Kollman. P-A. / Classification: refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: the structures are based on a total of 1773 NOE restraints, 80 dihedral angle restraints
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformers submitted total number: 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://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