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- EMDB-8808: Volta phase plate tomogram of SV(Cpx) + PM vesicle mixture -

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Basic information

Database: EMDB / ID: 8808
TitleVolta phase plate tomogram of SV(Cpx) + PM vesicle mixture
SampleSynaptic protein complexes
SourceRattus norvegicus / mammal / Brown rat (Wikipedia) /
Map dataTomogram of SV(Cpx) PM vesicle mixtures
Methodelectron tomography
AuthorsGipson P
CitationProc. Natl. Acad. Sci. U.S.A., 2017, 114, 9110-9115

Proc. Natl. Acad. Sci. U.S.A., 2017, 114, 9110-9115 Yorodumi Papers
Morphologies of synaptic protein membrane fusion interfaces.
Preeti Gipson / Yoshiyuki Fukuda / Radostin Danev / Ying Lai / Dong-Hua Chen / Wolfgang Baumeister / Axel T Brunger

DateDeposition: Jul 4, 2017 / Header (metadata) release: Aug 2, 2017 / Map release: Aug 2, 2017 / Last update: Sep 6, 2017

Structure visualization

  • Simplified surface model
  • Imaged by Jmol
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Supplemental images

Downloads & links


Fileemd_8808.map.gz (map file in CCP4 format, 398070 KB)
Projections & slices

Image control

AxesZ (Sec.)Y (Row.)X (Col.)
117 pix
6.84 Å/pix.
= 800.28 Å
825 pix
6.84 Å/pix.
= 5643. Å
1031 pix
6.84 Å/pix.
= 7052.04 Å



Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 6.84 Å
Contour Level:1.47 (by author)
Minimum - Maximum-3.8474927 - 7.743206
Average (Standard dev.)-0.0007023698 (0.56256)


Space Group Number1
Map Geometry
Axis orderXYZ
CellA: 7052.04 Å / B: 5643 Å / C: 800.28 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z1031825117
origin x/y/z0.0000.0000.000
length x/y/z7052.0405643.000800.280
start NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
D min/max/mean-3.8477.743-0.001

Supplemental data

Sample components

Entire Synaptic protein complexes

EntireName: Synaptic protein complexes / Number of components: 1

Component #1: protein, Synaptic protein complexes

ProteinName: Synaptic protein complexes / Recombinant expression: No
SourceSpecies: Rattus norvegicus / mammal / Brown rat (Wikipedia) /
Source (engineered)Expression System: Escherichia coli-pichia pastoris shuttle vector ppparg4 / bacteria / image: Escherichia coli

Experimental details

Sample preparation

Specimen stateparticle
Sample solutionpH: 7
VitrificationCryogen name: ETHANE

Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 0.632 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

Image processing

ProcessingMethod: electron tomography / Number of sections: 130

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