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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-11411 | |||||||||
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Title | Native putative NMDAR type glutamate receptor, model guided | |||||||||
![]() | Averaged density map. | |||||||||
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Biological species | ![]() ![]() | |||||||||
Method | subtomogram averaging / cryo EM / Resolution: 33.673847 Å | |||||||||
![]() | Martinez A / Lucic V | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() 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 |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 964 KB | ![]() | |
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Header (meta data) | ![]() ![]() | 12.7 KB 12.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 2.4 KB | Display | ![]() |
Images | ![]() | 32.3 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Map
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Annotation | Averaged density map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 6.84 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : Native putative NMDA-type ionotropic glutamate receptor imaged at...
Entire | Name: Native putative NMDA-type ionotropic glutamate receptor imaged at excitatory neocortical rodent synapses |
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Components |
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-Supramolecule #1: Native putative NMDA-type ionotropic glutamate receptor imaged at...
Supramolecule | Name: Native putative NMDA-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 NMDA receptor particles. By using PDB-6MMP ...Details: Postsynaptic complexes were detected by Morse density tracing and classified by Affinity propagation (both implemented in PySeg) to obtain putative NMDA receptor particles. By using PDB-6MMP as reference model, the structure ware further refined and classified in 3D with Relion. |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 400 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | subtomogram averaging |
Aggregation state | cell |
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Sample preparation
Concentration | 0.7 mg/mL |
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Buffer | pH: 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 |
Grid | Model: Quantifoil / Support film - Material: CARBON / Support film - topology: HOLEY |
Vitrification | Cryogen name: ETHANE / Chamber temperature: 300 K / Instrument: HOMEMADE PLUNGER |
Details | Neocortical synaptosomal fraction |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 1.66 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |