[English] 日本語
Yorodumi
- PDB-1zok: PDZ1 Domain Of Synapse Associated Protein 97 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zok
TitlePDZ1 Domain Of Synapse Associated Protein 97
ComponentsPresynaptic protein SAP97Synapse
KeywordsMEMBRANE PROTEIN / PDZ / PDZ1 / SAP97 / Synapse Associated Protein 97 / Beta Strand / Helix
Function / homology
Function and homology information


tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade ...tissue morphogenesis / regulation of protein localization to synapse / regulation of potassium ion import / L27 domain binding / regulation of potassium ion export across plasma membrane / MPP7-DLG1-LIN7 complex / membrane raft organization / hard palate development / establishment of centrosome localization / negative regulation of p38MAPK cascade / cortical microtubule organization / embryonic skeletal system morphogenesis / astral microtubule organization / structural constituent of postsynaptic density / lateral loop / reproductive structure development / myelin sheath abaxonal region / immunological synapse formation / peristalsis / cell projection membrane / paranode region of axon / smooth muscle tissue development / bicellular tight junction assembly / Trafficking of AMPA receptors / positive regulation of potassium ion transport / Activation of Ca-permeable Kainate Receptor / node of Ranvier / regulation of ventricular cardiac muscle cell action potential / protein-containing complex localization / establishment or maintenance of epithelial cell apical/basal polarity / amyloid precursor protein metabolic process / endothelial cell proliferation / RAF/MAP kinase cascade / Synaptic adhesion-like molecules / neurotransmitter receptor localization to postsynaptic specialization membrane / lens development in camera-type eye / ureteric bud development / regulation of myelination / cortical actin cytoskeleton organization / branching involved in ureteric bud morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / positive regulation of actin filament polymerization / receptor clustering / postsynaptic density, intracellular component / microvillus / kinesin binding / immunological synapse / basement membrane / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / lateral plasma membrane / Unblocking of NMDA receptors, glutamate binding and activation / bicellular tight junction / potassium channel regulator activity / phosphatase binding / T cell proliferation / cellular response to brain-derived neurotrophic factor stimulus / negative regulation of T cell proliferation / T-tubule / ionotropic glutamate receptor binding / actin filament polymerization / regulation of membrane potential / T cell activation / basal plasma membrane / phosphatidylinositol 3-kinase/protein kinase B signal transduction / synaptic membrane / actin filament organization / PDZ domain binding / protein localization to plasma membrane / postsynaptic density membrane / positive regulation of protein localization to plasma membrane / neuromuscular junction / protein localization / negative regulation of ERK1 and ERK2 cascade / cytoplasmic side of plasma membrane / cell-cell adhesion / synaptic vesicle membrane / cerebral cortex development / regulation of protein localization / negative regulation of epithelial cell proliferation / cell-cell junction / cell junction / presynaptic membrane / regulation of cell shape / chemical synaptic transmission / postsynaptic membrane / basolateral plasma membrane / cell population proliferation / microtubule / transmembrane transporter binding / postsynaptic density / molecular adaptor activity / cell adhesion / neuron projection / membrane raft / apical plasma membrane / neuronal cell body / dendrite / synapse / glutamatergic synapse / positive regulation of cell population proliferation
Similarity search - Function
L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors ...L27-1 / L27_1 / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Polyubiquitination (PEST) N-terminal domain of MAGUK / Disks large homologue 1, N-terminal PEST domain / Polyubiquitination (PEST) N-terminal domain of MAGUK / PDZ-associated domain of NMDA receptors / PDZ-associated domain of NMDA receptors / Disks large 1-like / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ domain / Pdz3 Domain / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Roll / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
Disks large homolog 1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / torsion angle dynamics
AuthorsWang, L. / Piserchio, A. / Mierke, D.F.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural Characterization of the Intermolecular Interactions of Synapse-associated Protein-97 with the NR2B Subunit of N-Methyl-D-aspartate Receptors.
Authors: Wang, L. / Piserchio, A. / Mierke, D.F.
History
DepositionMay 13, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 2, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Presynaptic protein SAP97


Theoretical massNumber of molelcules
Total (without water)10,0891
Polymers10,0891
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)1 / -structures with the least restraint violations
RepresentativeModel #1fewest violations

-
Components

#1: Protein Presynaptic protein SAP97 / Synapse / Synapse-associated protein 97 / SAP-97 / Discs / large homolog 1


Mass: 10089.323 Da / Num. of mol.: 1 / Fragment: PDZ1 domain (residues 221-313)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: Q62696

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 3D 15N-separated NOESY

-
Sample preparation

DetailsContents: 1mM C13-N15 PDZ1 of SAP97 in 20mM phosphate buffer, 10% D2O, 90% H2O
Solvent system: 10% D2O, 90% H2O
Sample conditionsIonic strength: No salt / pH: 7.4 / Pressure: Normal air pressure / Temperature: 298 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker AVANCE / Manufacturer: Bruker / Model: AVANCE / Field strength: 600 MHz

-
Processing

NMR software
NameVersionDeveloperClassification
CNS1.1A.T.Brunger, P.D.Adams, G.M.Clore, W.L.Delano, P.Gros, R.W.Grosse-Kunstleve, J.-S.Jiang, J.Kuszewski, M.Nilges, N.S.Pannu, R.J.Read, L.M.Rice, T.Simonson, G.L.Warrenstructure solution
NMRPipe2.3F. Delaglio, S. Grzesiek, G. W. Vuister, G. Zhu, J. Pfeifer and A. Baxprocessing
XwinNMR3Bruker Biospincollection
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers 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