[English] 日本語
Yorodumi
- PDB-1gm1: Second PDZ Domain (PDZ2) of PTP-BL -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1gm1
TitleSecond PDZ Domain (PDZ2) of PTP-BL
ComponentsPROTEIN TYROSINE PHOSPHATASE
KeywordsHYDROLASE / PDZ / PTP-BL / FAS INTERACTION / LIM INTERACTION / STRUCTURAL PROTEIN / CYTOSKELETON
Function / homology
Function and homology information


RND3 GTPase cycle / negative regulation of excitatory synapse assembly / RND2 GTPase cycle / RND1 GTPase cycle / Synthesis of PIPs at the plasma membrane / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of protein phosphorylation ...RND3 GTPase cycle / negative regulation of excitatory synapse assembly / RND2 GTPase cycle / RND1 GTPase cycle / Synthesis of PIPs at the plasma membrane / phosphatidylinositol 3-kinase regulatory subunit binding / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity / negative regulation of protein phosphorylation / lamellipodium / cell body / midbody / cytoskeleton / nucleus / cytoplasm
Similarity search - Function
Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal ...Tyrosine-protein phosphatase non-receptor type 13 / Unstructured linker region on PTN13 protein between PDZ / : / KIND domain / KIND domain profile. / kinase non-catalytic C-lobe domain / FERM, C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM C-terminal PH-like domain / FERM, N-terminal / FERM N-terminal domain / FERM central domain / FERM/acyl-CoA-binding protein superfamily / PDZ domain / Pdz3 Domain / FERM central domain / FERM superfamily, second domain / FERM domain / FERM domain profile. / Band 4.1 domain / Band 4.1 homologues / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Ubiquitin-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Tyrosine-protein phosphatase non-receptor type 13
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
MethodSOLUTION NMR / SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS
AuthorsWalma, T. / Tessari, M. / Aelen, J. / Schepens, J. / Hendriks, W. / Vuister, G.W.
CitationJournal: J. Mol. Biol. / Year: 2002
Title: Structure, dynamics and binding characteristics of the second PDZ domain of PTP-BL.
Authors: Walma, T. / Spronk, C.A. / Tessari, M. / Aelen, J. / Schepens, J. / Hendriks, W. / Vuister, G.W.
History
DepositionSep 6, 2001Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2002Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 28, 2018Group: Database references / Source and taxonomy / Category: citation / citation_author / entity_src_gen
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 15, 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN TYROSINE PHOSPHATASE


Theoretical massNumber of molelcules
Total (without water)9,7671
Polymers9,7671
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)35 / 200LOWEST ENERGY
RepresentativeModel #9

-
Components

#1: Protein PROTEIN TYROSINE PHOSPHATASE / NONRECEPTOR-TYPE / 13 / PROTEIN-TYROSINE PHOSPHATASE RIP / PHOSPHOPROTEIN PHOSPHATASE / PROTEIN- ...NONRECEPTOR-TYPE / 13 / PROTEIN-TYROSINE PHOSPHATASE RIP / PHOSPHOPROTEIN PHOSPHATASE / PROTEIN-TYROSINE-PHOSPHATASE / PHOSPHOTYROSINE PHOSPHATASE / PTPASE / PTP36 / BAS-LIKE


Mass: 9767.062 Da / Num. of mol.: 1 / Fragment: PDZ2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MUS MUSCULUS (house mouse) / Plasmid: PET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q64512, protein-tyrosine-phosphatase

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
11115N NOESY-HSQC
12113C NOESYHSQC
13113C NOESY-TROSY
141HNHA
151HCACO[N]
NMR detailsText: THE ENSEMBLE WAS DETERMINED USING 3D TRIPLE RESONANCE NMR SPECTROSCOPY USING SINGLE AND DOUBLE-LABELED PDZ2.

-
Sample preparation

Sample conditionsIonic strength: 100 / pH: 6.3 / Pressure: 1 atm / Temperature: 298 K
Crystal grow
*PLUS
Method: other / Details: NMR

-
NMR measurement

NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

-
Processing

NMR software
NameDeveloperClassification
X-PLORBRUNGERrefinement
X-PLORstructure solution
RefinementMethod: SIMULATED ANNEALING, RESTRAINED MOLECULAR DYNAMICS / Software ordinal: 1
Details: RESTRAINED MOLECULAR DYNAMICS WAS USED IN THE REFINEMENT PROTOCOL.
NMR ensembleConformer selection criteria: LOWEST ENERGY / Conformers calculated total number: 200 / Conformers submitted total number: 35

+
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