[English] 日本語
Yorodumi
- PDB-1u39: Auto-inhibition Mechanism of X11s/Mints Family Scaffold Proteins ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1u39
TitleAuto-inhibition Mechanism of X11s/Mints Family Scaffold Proteins Revealed by the Closed Conformation of the Tandem PDZ Domains
Componentsamyloid beta A4 precursor protein-binding, family A, member 1
KeywordsPROTEIN TRANSPORT / X11s/Mints / PDZ domain / scaffold protein / protein trafficking
Function / homology
Function and homology information


gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport ...gamma-aminobutyric acid secretion / Dopamine Neurotransmitter Release Cycle / glutamate secretion / axo-dendritic transport / Assembly and cell surface presentation of NMDA receptors / Neurexins and neuroligins / presynaptic active zone membrane / presynaptic modulation of chemical synaptic transmission / locomotory behavior / intracellular protein transport / Schaffer collateral - CA1 synapse / multicellular organism growth / synaptic vesicle / nervous system development / amyloid-beta binding / regulation of gene expression / protein-containing complex assembly / chemical synaptic transmission / in utero embryonic development / dendritic spine / cell adhesion / glutamatergic synapse / perinuclear region of cytoplasm / Golgi apparatus / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. ...: / Phosphotyrosine interaction domain (PTB/PID) / Phosphotyrosine interaction domain (PID) profile. / Phosphotyrosine-binding domain, phosphotyrosine-interaction (PI) domain / PTB/PI domain / PDZ domain / Pdz3 Domain / PDZ domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / PH-like domain superfamily / Roll / Mainly Beta
Similarity search - Domain/homology
Amyloid-beta A4 precursor protein-binding family A member 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model type detailsminimized average
AuthorsFeng, W. / Long, J.-F. / Chan, L.-N. / He, C. / Fu, A. / Xia, J. / Ip, N.Y. / Zhang, M.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2005
Title: Autoinhibition of X11/Mint scaffold proteins revealed by the closed conformation of the PDZ tandem
Authors: Long, J.-F. / Feng, W. / Wang, R. / Chan, L.-N. / Ip, F.C. / Xia, J. / Ip, N.Y. / Zhang, M.
History
DepositionJul 21, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 26, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: 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: amyloid beta A4 precursor protein-binding, family A, member 1


Theoretical massNumber of molelcules
Total (without water)8,7201
Polymers8,7201
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 #1minimized average structure

-
Components

#1: Protein amyloid beta A4 precursor protein-binding, family A, member 1 / X11alpha/Mint1 / phosphotyrosine-binding/-interacting domain (PTB)-bearing protein / neuronal ...X11alpha/Mint1 / phosphotyrosine-binding/-interacting domain (PTB)-bearing protein / neuronal munc18-1-interacting protein 1 / neuron-specific X11 protein / adaptor protein X11alpha


Mass: 8720.254 Da / Num. of mol.: 1 / Fragment: PDZ2 domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET32a / Production host: Escherichia coli (E. coli) / References: UniProt: Q02410

-
Experimental details

-
Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 15N-separated NOESY
122HNCO, HN(CA)CB, CBCA(CO)NH
1333D 13C-separated NOESY

-
Sample preparation

Details
Solution-IDContentsSolvent system
11.0mM uniformly 15N labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
21.0mM uniformly 15N/13C labelled PDZ2 in 90% H2O, 10% D2O; 100mM potassium phosphate90% H2O/10% D2O
31.0mM uniformly 15N/13C labelled PDZ2 in 99.9% D2O; 100mM potassium phosphate99.9% D2O
Sample conditionsIonic strength: 100mM potassium phosphate / pH: 6.5 / Pressure: 1 atm / Temperature: 303 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
NameVersionDeveloperClassification
CNS1.1Brunger, A.T.structure solution
CNS1.1Brunger, A.T.refinement
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://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