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- EMDB-11404: Native putative AMPA-type ionotropic glutamate receptor, de novo -

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Basic information

Entry
Database: EMDB / ID: EMD-11404
TitleNative putative AMPA-type ionotropic glutamate receptor, de novo
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: 33.673847 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

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.199
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.199
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11404.png

Downloads & links

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Map

FileDownload / File: emd_11404.map.gz / Format: CCP4 / Size: 1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAveraged density map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
6.84 Å/pix.
x 64 pix.
= 437.76 Å		6.84 Å/pix.
x 64 pix.
= 437.76 Å		6.84 Å/pix.
x 64 pix.
= 437.76 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 6.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.199 / Movie #1: 0.199
Minimum - Maximum-1.3918533 - 1.712388
Average (Standard dev.)0.00067797146 (±0.14679614)
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-1.3921.7120.001

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Supplemental data

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Sample components

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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

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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
Source (natural)Organism: Rattus norvegicus (Norway rat) / Organ: brain / Tissue: neocortex / Organelle: excitatory synapse / Location in cell: postsynaptic
Molecular weightTheoretical: 400 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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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 R2/2 / Material: COPPER / Mesh: 100 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber temperature: 300 K / Instrument: HOMEMADE PLUNGER
DetailsNeocortical synaptosomal fraction

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Electron microscopy

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

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 33.673847 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.1) / Number subtomograms used: 566
ExtractionNumber tomograms: 17 / Number images used: 5688 / Reference model: De novo / Method: Automated / Software - Name: PySeg
Details: Morse density tracing and affinity propagation classification
Final 3D classificationNumber classes: 4 / Avg.num./class: 206 / Software - Name: PySEG
Details: Classification by Affinity propagation clustering of 2D rotation averages around axis normal to the plasma membrane
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2.1)
FSC plot (resolution estimation)

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