[English] 日本語
Yorodumi
- EMDB-43374: CryoET of VSV incubated with liposomes at pH 5.5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43374
TitleCryoET of VSV incubated with liposomes at pH 5.5
Map dataTomogram TS3016 from the 90s post-incubation dataset, pertaining to Fig. 2A.
Sample
  • Virus: Vesicular stomatitis Indiana virus strain San Juan
KeywordsVirus / Liposome / Fusion / Class III Fusion / VSV / VSV G
Biological speciesVesicular stomatitis Indiana virus strain San Juan
Methodelectron tomography / cryo EM
AuthorsSi Z / Xia X / Tang S / Milojevic L
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM071940 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI171426 United States
CitationJournal: To be Published
Title: Capturing Intermediates and Membrane Remodeling during Class III Fusion
Authors: Milojevic L / Si Z / Xia X / Chen L / He Y / Tang S / Luo M / Zhou ZH
History
DepositionJan 15, 2024-
Header (metadata) releaseAug 7, 2024-
Map releaseAug 7, 2024-
UpdateAug 7, 2024-
Current statusAug 7, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43374.png

Downloads & links

-
Map

FileDownload / File: emd_43374.map.gz / Format: CCP4 / Size: 831.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTomogram TS3016 from the 90s post-incubation dataset, pertaining to Fig. 2A.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.16 Å/pix.
x 333 pix.
= 2717.28 Å		8.16 Å/pix.
x 960 pix.
= 7833.6 Å		8.16 Å/pix.
x 682 pix.
= 5565.12 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 8.16 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-6.527553 - 26.656967000000002
Average (Standard dev.)0.4765678 (±0.33842728)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions960682333
Spacing682960333
CellA: 5565.12 Å / B: 7833.5996 Å / C: 2717.28 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Vesicular stomatitis Indiana virus strain San Juan

EntireName: Vesicular stomatitis Indiana virus strain San Juan
Components
  • Virus: Vesicular stomatitis Indiana virus strain San Juan

-
Supramolecule #1: Vesicular stomatitis Indiana virus strain San Juan

SupramoleculeName: Vesicular stomatitis Indiana virus strain San Juan / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 11285
Sci species name: Vesicular stomatitis Indiana virus strain San Juan
Virus type: VIRION / Virus isolate: OTHER / Virus enveloped: Yes / Virus empty: No

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 5.5
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Support film - Material: CARBON / Support film - topology: LACEY
VitrificationCryogen name: ETHANE
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Cell Microscopy Core, Department of Cell Biology, University Medical Center Utrecht
Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionNumber images used: 36

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
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.
  • 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

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more