[English] 日本語
Yorodumi
- PDB-1y76: Solution Structure of Patj/Pals1 L27 Domain Complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1y76
TitleSolution Structure of Patj/Pals1 L27 Domain Complex
Components
  • MAGUK p55 subfamily member 5
  • protein associated to tight junctions
KeywordsTRANSPORT PROTEIN / L27 domain / scaffold protein / protein assembly / cell polarity
Function / homology
Function and homology information


subapical complex / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction ...subapical complex / protein localization to myelin sheath abaxonal region / SARS-CoV-1 targets PDZ proteins in cell-cell junction / establishment or maintenance of polarity of embryonic epithelium / myelin assembly / morphogenesis of an epithelial sheet / tight junction assembly / Tight junction interactions / microtubule organizing center organization / SARS-CoV-2 targets PDZ proteins in cell-cell junction / lateral loop / myelin sheath adaxonal region / regulation of transforming growth factor beta receptor signaling pathway / Schmidt-Lanterman incisure / apicolateral plasma membrane / peripheral nervous system myelin maintenance / establishment or maintenance of epithelial cell apical/basal polarity / apical junction complex / generation of neurons / central nervous system neuron development / dendrite development / bicellular tight junction / endomembrane system / regulation of microtubule cytoskeleton organization / myelination / endoplasmic reticulum-Golgi intermediate compartment membrane / protein localization to plasma membrane / adherens junction / intracellular protein transport / cerebral cortex development / apical part of cell / gene expression / cytoplasmic vesicle / perikaryon / postsynaptic density / cell adhesion / intracellular signal transduction / apical plasma membrane / protein domain specific binding / axon / glutamatergic synapse / synapse / dendrite / Golgi apparatus / protein-containing complex / extracellular exosome / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
L27 domain / L27-N / Multiple PDZ domain protein / MPP5, SH3 domain / L27_N / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / L27 domain, C-terminal / L27 domain ...L27 domain / L27-N / Multiple PDZ domain protein / MPP5, SH3 domain / L27_N / Unstructured region 10 on multiple PDZ protein / L27-2 / L27_2 / L27 domain, C-terminal / L27 domain / domain in receptor targeting proteins Lin-2 and Lin-7 / L27 domain / L27 domain profile. / L27 domain superfamily / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Variant SH3 domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / PDZ 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 / Helix Hairpins / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Multiple PDZ domain protein / Protein PALS1
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Homo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Long, J.-F. / Zhang, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2005
Title: A unified assembly mode revealed by the structures of tetrameric L27 domain complexes formed by mLin-2/mLin-7 and Patj/Pals1 scaffold proteins.
Authors: Feng, W. / Long, J.F. / Zhang, M.
History
DepositionDec 8, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 19, 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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: protein associated to tight junctions
B: MAGUK p55 subfamily member 5
C: protein associated to tight junctions
D: MAGUK p55 subfamily member 5


Theoretical massNumber of molelcules
Total (without water)27,8404
Polymers27,8404
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)20 / 200structures with the lowest energy
RepresentativeModel #10minimized average structure

-
Components

#1: Protein protein associated to tight junctions / Patj


Mass: 7068.132 Da / Num. of mol.: 2 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: O55164
#2: Protein MAGUK p55 subfamily member 5 / Pals1


Mass: 6851.812 Da / Num. of mol.: 2 / Fragment: L27 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8N3R9

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D NOESY
1223D 15N-separated NOESY
133HNCO, HNCA, HN(CO)CA, HN(CA)CB, CBCA(CO)NH
1443D 13C-separated NOESY
15513C-HSQC

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.5mM unlabelled L27P/L27NP complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
21.5mM uniformly 15N labelled L27P/L27NP complex in 90% H2O/10% D2O; 100mM potassium phosphate90% H2O/10% D2O
31.5mM uniformly 15N/13C labelled L27P/L27NP complex in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
41.5mM uniformly 15N/13C labelled L27P/L27NP complex in 99.9% D2O; 100mM potassium phosphate99.9% D2O
51.5mM 10% 13C labelled L27P/L27NP complex in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 6.5 / Pressure: 1 atm / Temperature: 318 K

-
NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Varian INOVA / Manufacturer: Varian / Model: INOVA / Field strength: 750 MHz

-
Processing

NMR software
NameVersionClassification
CNS1.1structure solution
CNS1.1refinement
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

+
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://pdbjlvh1.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