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- EMDB-30364: Cryo-electron tomography of an excitatory synapse in cultured rat... -

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Basic information

Entry
Database: EMDB / ID: EMD-30364
TitleCryo-electron tomography of an excitatory synapse in cultured rat hippocampal neurons
Map data
Sample
  • Cell: hippocampal neuronal synapse
Biological speciesRattus sp. (rats)
Methodelectron tomography / cryo EM
AuthorsTao C-L / Liu Y-T / Sun R / Zhang B / Qi L / Shivakoti S / Tian C-L / Zhang P / Lau P-M / Zhou ZH / Bi G-Q
Citation
Journal: To Be Published
Title: Cryo-electron tomography of an excitatory synapse in cultured rat hippocampal neurons
Authors: Tao CL / Liu YT / Sun R / Zhang B / Qi L / Shivakoti S / Tian CL / Zhang P / Lau PM / Zhou ZH / Bi GQ
#1: Journal: J. Neurosci. / Year: 2018
Title: Differentiation and Characterization of Excitatory and Inhibitory Synapses by Cryo-electron Tomography and Correlative Microscopy.
Authors: Tao CL / Liu YT / Sun R / Zhang B / Qi L / Shivakoti S / Tian CL / Zhang P / Lau PM / Zhou ZH / Bi GQ
History
DepositionJul 2, 2020-
Header (metadata) releaseJul 7, 2021-
Map releaseJul 7, 2021-
UpdateJul 7, 2021-
Current statusJul 7, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
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Supplemental images

emd_30364.png

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Map

FileDownload / File: emd_30364.map.gz / Format: CCP4 / Size: 143.8 MB / Type: IMAGE STORED AS SIGNED BYTE
Voxel sizeX=Y=Z: 26.1 Å
Density
Minimum - Maximum-128.0 - 126.0
Average (Standard dev.)60.184612 (±6.2655435)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin1057
Dimensions620640380
Spacing640620380
CellA: 16704.0 Å / B: 16182.0 Å / C: 9918.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z26.126.126.1
M x/y/z640620380
origin x/y/z0.0000.0000.000
length x/y/z16704.00016182.0009918.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-210-210-210
NX/NY/NZ420420420
MAP C/R/S123
start NC/NR/NS0157
NC/NR/NS640620380
D min/max/mean-128.000126.00060.185

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Supplemental data

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Sample components

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Entire : hippocampal neuronal synapse

EntireName: hippocampal neuronal synapse
Components
  • Cell: hippocampal neuronal synapse

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Supramolecule #1: hippocampal neuronal synapse

SupramoleculeName: hippocampal neuronal synapse / type: cell / ID: 1 / Parent: 0
Details: excitatory synapse in cultured rat hippocampal neurons
Source (natural)Organism: Rattus sp. (rats)

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Experimental details

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Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

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Sample preparation

BufferpH: 7.3
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Center for Molecular Medicine | University Medical Center Utrecht
Diameter: 15 nm

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / 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 reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD / Number images used: 64

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