[English] 日本語
Yorodumi
- PDB-1kjw: SH3-Guanylate Kinase Module from PSD-95 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1kjw
TitleSH3-Guanylate Kinase Module from PSD-95
ComponentsPOSTSYNAPTIC DENSITY PROTEIN 95
KeywordsNEUROPEPTIDE / PROTEIN-PROTEIN INTERACTION / SCAFFOLD
Function / homology
Function and homology information


RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / Neurexins and neuroligins / beta-1 adrenergic receptor binding / neuroligin family protein binding / structural constituent of postsynaptic density / proximal dendrite / positive regulation of neuron projection arborization / synaptic vesicle maturation / regulation of grooming behavior / receptor localization to synapse / cellular response to potassium ion / protein localization to synapse / cerebellar mossy fiber / vocalization behavior / LGI-ADAM interactions / Trafficking of AMPA receptors / neuron spine / dendritic branch / Activation of Ca-permeable Kainate Receptor / AMPA glutamate receptor clustering / frizzled binding / dendritic spine morphogenesis / juxtaparanode region of axon / establishment or maintenance of epithelial cell apical/basal polarity / negative regulation of receptor internalization / dendritic spine organization / postsynaptic neurotransmitter receptor diffusion trapping / neuron projection terminus / acetylcholine receptor binding / positive regulation of synapse assembly / regulation of NMDA receptor activity / Synaptic adhesion-like molecules / positive regulation of dendrite morphogenesis / RAF/MAP kinase cascade / beta-2 adrenergic receptor binding / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / regulation of neuronal synaptic plasticity / kinesin binding / extrinsic component of cytoplasmic side of plasma membrane / positive regulation of excitatory postsynaptic potential / AMPA glutamate receptor complex / social behavior / neuromuscular process controlling balance / positive regulation of protein tyrosine kinase activity / excitatory synapse / D1 dopamine receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of synaptic transmission / glutamate receptor binding / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / kinase binding / cell-cell adhesion / postsynaptic density membrane / regulation of long-term neuronal synaptic plasticity / establishment of protein localization / neuromuscular junction / cerebral cortex development / cell junction / cell-cell junction / synaptic vesicle / positive regulation of cytosolic calcium ion concentration / basolateral plasma membrane / protein phosphatase binding / scaffold protein binding / protein-containing complex assembly / chemical synaptic transmission / postsynaptic membrane / postsynapse / dendritic spine / postsynaptic density / neuron projection / signaling receptor binding / glutamatergic synapse / synapse / dendrite / protein-containing complex binding / protein kinase binding / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Guanylate Kinase phosphate binding domain / Guanylate Kinase phosphate binding domain / 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 phosphate binding domain / Guanylate Kinase phosphate binding domain / 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. / SH3 Domains / PDZ domain / SH3 domain / PDZ domain profile. / Domain present in PSD-95, Dlg, and ZO-1/2. / PDZ domain / PDZ superfamily / SH3 type barrels. / Src homology 3 domains / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / P-loop containing nucleotide triphosphate hydrolases / Roll / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsMcGee, A.W. / Dakoji, S.R. / Olsen, O. / Bredt, D.S. / Lim, W.A. / Prehoda, K.E.
CitationJournal: Mol Cell / Year: 2001
Title: Structure of the SH3-guanylate kinase module from PSD-95 suggests a mechanism for regulated assembly of MAGUK scaffolding proteins.
Authors: A W McGee / S R Dakoji / O Olsen / D S Bredt / W A Lim / K E Prehoda /
Abstract: Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit ...Membrane-associated guanylate kinases (MAGUKs), such as PSD-95, are modular scaffolds that organize signaling complexes at synapses and other cell junctions. MAGUKs contain PDZ domains, which recruit signaling proteins, as well as a Src homology 3 (SH3) and a guanylate kinase-like (GK) domain, implicated in scaffold oligomerization. The crystal structure of the SH3-GK module from PSD-95 reveals that these domains form an integrated unit: the SH3 fold comprises noncontiguous sequence elements divided by a hinge region and the GK domain. These elements compose two subdomains that can assemble in either an intra- or intermolecular fashion to complete the SH3 fold. We propose a model for MAGUK oligomerization in which complementary SH3 subdomains associate by 3D domain swapping. This model provides a possible mechanism for ligand regulation of oligomerization.
History
DepositionDec 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 9, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 31, 2018Group: Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: POSTSYNAPTIC DENSITY PROTEIN 95
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4333
Polymers34,2411
Non-polymers1922
Water2,270126
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.509, 60.509, 209.956
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

-
Components

#1: Protein POSTSYNAPTIC DENSITY PROTEIN 95 / PSD-95 / POSTSYNAPTIC PROTEIN SAP90 / SYNAPSE-ASSOCIATED PROTEIN 90


Mass: 34241.367 Da / Num. of mol.: 1 / Fragment: SH3 Domain/Guanylate Kinase Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Production host: Escherichia coli (E. coli) / References: UniProt: P31016
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.81 Å3/Da / Density % sol: 56.17 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulfate, PEG 4000, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 15K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion, sitting drop / Details: used microseeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
22 Mammonium sulfate1reservoir
32 %PEG4001reservoir
410 mMHEPES1reservoirpH7.0

-
Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. all: 37032 / Num. obs: 37032 / % possible obs: 99.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.8→1.9 Å / % possible all: 94
Reflection
*PLUS
Lowest resolution: 25 Å / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 94.4 % / Rmerge(I) obs: 0.351

-
Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SHARPphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MAD / Resolution: 1.8→25 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.25 3703 RANDOM
Rwork0.23 --
all-37032 -
obs-37032 -
Refinement stepCycle: LAST / Resolution: 1.8→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2393 0 10 126 2529
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 25 Å / σ(F): 0 / Rfactor obs: 0.23 / Rfactor Rfree: 0.25 / Rfactor Rwork: 0.23
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.08
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

+
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