[English] 日本語
Yorodumi
- EMDB-1761: Single particle analysis of PSD-95 in negative stain -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1761
TitleSingle particle analysis of PSD-95 in negative stain
Map data3d map of PSD-95
Sample
  • Sample: Rat PSD-95
  • Protein or peptide: PSD-95
KeywordsScaffold protein / Membrane associated Guanylate Kinase / PDZ / SH3
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 / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation ...RHO GTPases activate CIT / positive regulation of AMPA glutamate receptor clustering / neuronal ion channel clustering / P2Y1 nucleotide receptor binding / beta-1 adrenergic receptor binding / Neurexins and neuroligins / neuroligin family protein binding / regulation of grooming behavior / structural constituent of postsynaptic density / synaptic vesicle maturation / positive regulation of neuron projection arborization / receptor localization to synapse / vocalization behavior / neuron spine / cerebellar mossy fiber / AMPA glutamate receptor clustering / protein localization to synapse / positive regulation of dendrite morphogenesis / proximal dendrite / Trafficking of AMPA receptors / dendritic branch / LGI-ADAM interactions / Activation of Ca-permeable Kainate Receptor / dendritic spine morphogenesis / negative regulation of receptor internalization / frizzled binding / neuron projection terminus / acetylcholine receptor binding / juxtaparanode region of axon / regulation of NMDA receptor activity / dendritic spine organization / cellular response to potassium ion / RAF/MAP kinase cascade / positive regulation of synapse assembly / beta-2 adrenergic receptor binding / NMDA selective glutamate receptor signaling pathway / Synaptic adhesion-like molecules / neuromuscular process controlling balance / neurotransmitter receptor localization to postsynaptic specialization membrane / cortical cytoskeleton / locomotory exploration behavior / AMPA glutamate receptor complex / excitatory synapse / social behavior / regulation of neuronal synaptic plasticity / kinesin binding / glutamate receptor binding / Unblocking of NMDA receptors, glutamate binding and activation / positive regulation of excitatory postsynaptic potential / D1 dopamine receptor binding / positive regulation of synaptic transmission / regulation of postsynaptic membrane neurotransmitter receptor levels / ionotropic glutamate receptor binding / dendrite cytoplasm / synaptic membrane / cell periphery / PDZ domain binding / neuromuscular junction / establishment of protein localization / cell-cell adhesion / regulation of long-term neuronal synaptic plasticity / postsynaptic density membrane / cerebral cortex development / kinase binding / synaptic vesicle / cell-cell junction / cell junction / nervous system development / positive regulation of cytosolic calcium ion concentration / protein-containing complex assembly / scaffold protein binding / protein phosphatase binding / chemical synaptic transmission / dendritic spine / postsynaptic membrane / postsynapse / neuron projection / postsynaptic density / signaling receptor binding / synapse / dendrite / protein kinase binding / protein-containing complex binding / glutamatergic synapse / endoplasmic reticulum / membrane / plasma membrane / cytoplasm / cytosol
Similarity search - Function
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 / Disks large 1-like / : / Guanylate kinase, conserved site / Guanylate kinase-like signature. ...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 / 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 / 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 / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Disks large homolog 4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Methodsingle particle reconstruction / negative staining / Resolution: 22.9 Å
AuthorsFomina S / Howard TD / Sleator OK / Golovanova M / O'Ryan L / Leyland M / Grossmann JG / Collins RF / Prince SM
CitationJournal: Biochim Biophys Acta / Year: 2011
Title: Self-directed assembly and clustering of the cytoplasmic domains of inwardly rectifying Kir2.1 potassium channels on association with PSD-95.
Authors: Svetlana Fomina / Tina D Howard / Olivia K Sleator / Marina Golovanova / Liam O'Ryan / Mark L Leyland / J Günter Grossmann / Richard F Collins / Stephen M Prince /
Abstract: The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using ...The interaction of the extra-membranous domain of tetrameric inwardly rectifying Kir2.1 ion channels (Kir2.1NC(4)) with the membrane associated guanylate kinase protein PSD-95 has been studied using Transmission Electron Microscopy in negative stain. Three types of complexes were observed in electron micrographs corresponding to a 1:1 complex, a large self-enclosed tetrad complex and extended chains of linked channel domains. Using models derived from small angle X-ray scattering experiments in which high resolution structures from X-ray crystallographic and Nuclear Magnetic Resonance studies are positioned, the envelopes from single particle analysis can be resolved as a Kir2.1NC(4):PSD-95 complex and a tetrad of this unit (Kir2.1NC(4):PSD-95)(4). The tetrad complex shows the close association of the Kir2.1 cytoplasmic domains and the influence of PSD-95 mediated self-assembly on the clustering of these channels.
History
DepositionJul 13, 2010-
Header (metadata) releaseMar 11, 2011-
Map releaseJul 14, 2011-
UpdateSep 19, 2012-
Current statusSep 19, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-2xkx
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1761.png

Downloads & links

-
Map

FileDownload / File: emd_1761.map.gz / Format: CCP4 / Size: 422.9 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3d map of PSD-95
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.67 Å/pix.
x 48 pix.
= 176.016 Å		3.67 Å/pix.
x 48 pix.
= 176.016 Å		3.67 Å/pix.
x 48 pix.
= 176.016 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.667 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.88844132 - 3.87746572
Average (Standard dev.)0.0 (±0.303009)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-24-24-24
Dimensions484848
Spacing484848
CellA=B=C: 176.016 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.6673.6673.667
M x/y/z484848
origin x/y/z0.0000.0000.000
length x/y/z176.016176.016176.016
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS-24-24-24
NC/NR/NS484848
D min/max/mean-1.8883.8770.000

-
Supplemental data

-
Sample components

-
Entire : Rat PSD-95

EntireName: Rat PSD-95
Components
  • Sample: Rat PSD-95
  • Protein or peptide: PSD-95

-
Supramolecule #1000: Rat PSD-95

SupramoleculeName: Rat PSD-95 / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1
Molecular weightExperimental: 95 KDa / Theoretical: 78 KDa / Method: SDS-PAGE

-
Macromolecule #1: PSD-95

MacromoleculeName: PSD-95 / type: protein_or_peptide / ID: 1 / Name.synonym: PSD-95 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Rattus norvegicus (Norway rat) / synonym: Norway Rat / Location in cell: Membrane
Molecular weightExperimental: 95 KDa / Theoretical: 78 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pGEX-6P
SequenceGO: neuronal ion channel clustering / InterPro: Disks large 1-like

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration1 mg/mL
BufferpH: 7.5 / Details: 20mM Tris/HCl, 5mM DTT, 1mM EDTA,
StainingType: NEGATIVE
Details: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by ...Details: Samples were adsorbed onto freshly glow discharged carbon film grids. Sample solution was pipetted into the grid followed by blotting, de-ionized water was then applied for 10s followed by blotting, 2%w/v Uranyl Acetate solution was applied followed by a final blotting step.
GridDetails: 400 mesh Copper
VitrificationCryogen name: NONE / Instrument: OTHER

-
Electron microscopy

MicroscopeFEI TECNAI 10
DetailsLow dose
Image recordingCategory: FILM / Film or detector model: GENERIC FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 15 µm / Number real images: 2 / Details: none / Od range: 2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 100 kV / Electron source: TUNGSTEN HAIRPIN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 3.6 mm / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 43000
Sample stageSpecimen holder: Eucentric / Specimen holder model: PHILIPS ROTATION HOLDER

-
Image processing

DetailsParticles selected using model based picking using an ab-initio model from Small angle X-ray scattering
CTF correctionDetails: Paramters determined using Scattering curve
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 22.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN / Number images used: 7854
Final two d classificationNumber classes: 84

-
Atomic model buiding 1

Initial modelPDB ID:

1iu0

SoftwareName: Chimera
DetailsModel assembled using SAXS refinement and docked
RefinementSpace: REAL
Output model

PDB-2xkx:
Single particle analysis of PSD-95 in negative stain

-
Atomic model buiding 2

Initial modelPDB ID:

1qlc

SoftwareName: Chimera
DetailsModel assembled using SAXS refinement and docked
RefinementSpace: REAL
Output model

PDB-2xkx:
Single particle analysis of PSD-95 in negative stain

-
Atomic model buiding 3

Initial modelPDB ID:

1tp5

SoftwareName: Chimera
DetailsModel assembled using SAXS refinement and docked
RefinementSpace: REAL
Output model

PDB-2xkx:
Single particle analysis of PSD-95 in negative stain

-
Atomic model buiding 4

Initial modelPDB ID:

1kjw

SoftwareName: Chimera
DetailsModel assembled using SAXS refinement and docked
RefinementSpace: REAL
Output model

PDB-2xkx:
Single particle analysis of PSD-95 in negative stain

+
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