[English] 日本語
Yorodumi
- EMDB-8807: Volta phase plate tomogram of SV + PM vesicle mixture -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 8807
TitleVolta phase plate tomogram of SV + PM vesicle mixture
SampleSynaptic protein complexes
SourceRattus norvegicus / mammal / ドブネズミ, どぶねずみ /
Map dataTomogram of SV 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

Movie
  • Simplified surface model
  • Imaged by Jmol
  • Download
3D viewer


View / / Stereo:
Center
Zoom
Scale
Slabnear <=> far

fix: /
Orientation
Orientation Rotation
Misc. /
Show/hide
Supplemental images

Downloads & links

-
Map

Fileemd_8807.map.gz (map file in CCP4 format, 412366 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
112 pix
6.84 Å/pix.
= 766.08 Å
973 pix
6.84 Å/pix.
= 6655.32 Å
946 pix
6.84 Å/pix.
= 6470.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 6.84 Å
Density
Contour Level:1.47 (by author)
Minimum - Maximum-3.9321134 - 8.986888
Average (Standard dev.)0.00031601434 (0.5916984)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions973946112
Origin000
Limit972945111
Spacing946973112
CellA: 6470.64 Å / B: 6655.3203 Å / C: 766.08 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z6.846.846.84
M x/y/z946973112
origin x/y/z0.0000.0000.000
length x/y/z6470.6406655.320766.080
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS946973112
D min/max/mean-3.9328.9870.000

-
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 / ドブネズミ, どぶねずみ /
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

+
About Yorodumi

-
News

-
Oct 4, 2017. Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

Three pioneers of this field were awarded Nobel Prize in Chemistry 2017

  • Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
  • Joachim Frank (Columbia University, New York, USA) is a pioneer of single particle reconstruction, which is the most used reconstruction method for 3DEM structures in EMDB and EM entries in PDB. And also, he is a develper of Spider, which is one of the most famous software in this field, and is used for some EM Navigor data (e.g. map projection/slice images).
  • Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.

External links: The 2017 Nobel Prize in Chemistry - Press Release

-
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. See below links for details.
  • 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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi / EM Navigator (legacy version) / Yorodumi (legacy version)

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • All the functionalities will be ported from the levgacy version.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: Yorodumi (legacy version) / EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Yorodumi Papers / Jmol/JSmol / Changes in new EM Navigator and Yorodumi

Read more