[English] 日本語
Yorodumi
- EMDB-11406: Native putative AMPAR-type glutamate receptor, de novo 3D classif... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-11406
TitleNative putative AMPAR-type glutamate receptor, de novo 3D classification
Map dataAveraged density map.
Sample
  • Complex: Native putative AMPA-type ionotropic glutamate receptor imaged at excitatory neocortical rodent synapses
Biological speciesRattus norvegicus (Norway rat)
Methodsubtomogram averaging / cryo EM / Resolution: 31.268572 Å
AuthorsMartinez A / Lucic V
Funding supportEuropean Union, Spain, 2 items
OrganizationGrant numberCountry
European CommissionFP7 GA ERC-2012 SyG_318987 ToPAGEuropean Union
Seneca Foundation Spain
CitationJournal: Sci Adv / Year: 2021
Title: Trans-synaptic assemblies link synaptic vesicles and neuroreceptors.
Authors: Antonio Martinez-Sanchez / Ulrike Laugks / Zdravko Kochovski / Christos Papantoniou / Luca Zinzula / Wolfgang Baumeister / Vladan Lučić /
Abstract: Synaptic transmission is characterized by fast, tightly coupled processes and complex signaling pathways that require a precise protein organization, such as the previously reported nanodomain ...Synaptic transmission is characterized by fast, tightly coupled processes and complex signaling pathways that require a precise protein organization, such as the previously reported nanodomain colocalization of pre- and postsynaptic proteins. Here, we used cryo-electron tomography to visualize synaptic complexes together with their native environment comprising interacting proteins and lipids on a 2- to 4-nm scale. Using template-free detection and classification, we showed that tripartite trans-synaptic assemblies (subcolumns) link synaptic vesicles to postsynaptic receptors and established that a particular displacement between directly interacting complexes characterizes subcolumns. Furthermore, we obtained de novo average structures of ionotropic glutamate receptors in their physiological composition, embedded in plasma membrane. These data support the hypothesis that synaptic function is carried by precisely organized trans-synaptic units. It provides a framework for further exploration of synaptic and other large molecular assemblies that link different cells or cellular regions and may require weak or transient interactions to exert their function.
History
DepositionJul 16, 2020-
Header (metadata) releaseMay 26, 2021-
Map releaseMay 26, 2021-
UpdateMay 26, 2021-
Current statusMay 26, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.225
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.225
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11406.png

Downloads & links

-
Map

FileDownload / File: emd_11406.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged density map.
Voxel sizeX=Y=Z: 6.84 Å
Density
Contour LevelBy AUTHOR: 0.225 / Movie #1: 0.225
Minimum - Maximum-1.5194225 - 1.4183005
Average (Standard dev.)-0.00093137124 (±0.1686667)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions646464
Spacing646464
CellA=B=C: 437.76 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z646464
origin x/y/z0.0000.0000.000
length x/y/z437.760437.760437.760
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS646464
D min/max/mean-1.5191.418-0.001

-
Supplemental data

-
Sample components

-
Entire : Native putative AMPA-type ionotropic glutamate receptor imaged at...

EntireName: Native putative AMPA-type ionotropic glutamate receptor imaged at excitatory neocortical rodent synapses
Components
  • Complex: Native putative AMPA-type ionotropic glutamate receptor imaged at excitatory neocortical rodent synapses

-
Supramolecule #1: Native putative AMPA-type ionotropic glutamate receptor imaged at...

SupramoleculeName: Native putative AMPA-type ionotropic glutamate receptor imaged at excitatory neocortical rodent synapses
type: complex / ID: 1 / Parent: 0
Details: Postsynaptic complexes were detected by Morse density tracing and classified by Affinity propagation (both implemented in PySeg) to obtain putative AMPA receptor particles. Afterwards the ...Details: Postsynaptic complexes were detected by Morse density tracing and classified by Affinity propagation (both implemented in PySeg) to obtain putative AMPA receptor particles. Afterwards the averaged were further refined by 3D classification in Relion.
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: brain / Tissue: neocortex / Organelle: excitatory synapse / Location in cell: postsynaptic
Molecular weightTheoretical: 400 KDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

Concentration0.7 mg/mL
BufferpH: 7.4 / Component - Name: HEPES-buffered saline
Details: 140 mM NaCl, 5 mM KCl, 5 mM NaHCO3, 1.2 mM Na2HPO4, 1 mM MgCl2, 10 mM glucose, and 10 mM Hepes
GridModel: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber temperature: 300 K / Instrument: HOMEMADE PLUNGER
DetailsNeocortical synaptosomal fraction

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm
Specialist opticsEnergy filter - Slit width: 20 eV
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.66 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

ExtractionNumber tomograms: 17 / Number images used: 5688 / Reference model: De novo / Method: Automated / Software - details: PySeg
Details: Morse density tracing and affinity propagation classification
Final 3D classificationNumber classes: 4 / Avg.num./class: 206 / Software - Name: RELION (ver. 2.1) / Details: 3D classification by Relion
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 31.268572 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number subtomograms used: 317
FSC plot (resolution estimation)

+
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