[English] 日本語
Yorodumi
- EMDB-3868: Cryo-EM single particle reconstruction of Melbournevirus particle. -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3868
TitleCryo-EM single particle reconstruction of Melbournevirus particle.
Map dataMelbournevirus capsid(applied inner mask)
SampleMelbournevirus particle != Melbournevirus

Melbournevirus particle

  • Virus: Melbournevirus
Biological speciesMelbournevirus
Methodsingle particle reconstruction / cryo EM / Resolution: 26.3 Å
AuthorsOkamoto K / Miyazaki N / Reddy KNH / Hantke FM / Maia RNCF / Larsson SDD / Abergel C / Claverie JM / Hajdu J / Murata K / Svenda M
CitationJournal: Virology / Year: 2018
Title: Cryo-EM structure of a Marseilleviridae virus particle reveals a large internal microassembly.
Authors: Kenta Okamoto / Naoyuki Miyazaki / Hemanth K N Reddy / Max F Hantke / Filipe R N C Maia / Daniel S D Larsson / Chantal Abergel / Jean-Michel Claverie / Janos Hajdu / Kazuyoshi Murata / Martin Svenda /
Abstract: Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron ...Nucleocytoplasmic large DNA viruses (NCLDVs) blur the line between viruses and cells. Melbournevirus (MelV, family Marseilleviridae) belongs to a new family of NCLDVs. Here we present an electron cryo-microscopy structure of the MelV particle, with the large triangulation number T = 309 constructed by 3080 pseudo-hexagonal capsomers. The most distinct feature of the particle is a large and dense body (LDB) consistently found inside all particles. Electron cryo-tomography of 147 particles shows that the LDB is preferentially located in proximity to the probable lipid bilayer. The LDB is 30 nm in size and its density matches that of a genome/protein complex. The observed LDB reinforces the structural complexity of MelV, setting it apart from other NCLDVs.
History
DepositionSep 12, 2017-
Header (metadata) releaseDec 20, 2017-
Map releaseMar 14, 2018-
UpdateMar 14, 2018-
Current statusMar 14, 2018Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.6
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3868.png

Downloads & links

-
Map

FileDownload / File: emd_3868.map.gz / Format: CCP4 / Size: 2.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMelbournevirus capsid(applied inner mask)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.31 Å/pix.
x 840 pix.
= 2780.4 Å		3.31 Å/pix.
x 840 pix.
= 2780.4 Å		3.31 Å/pix.
x 840 pix.
= 2780.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.31 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.6 / Movie #1: 0.6
Minimum - Maximum-0.99535125 - 1.470726
Average (Standard dev.)-0.016885828 (±0.2911426)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions840840840
Spacing840840840
CellA=B=C: 2780.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.313.313.31
M x/y/z840840840
origin x/y/z0.0000.0000.000
length x/y/z2780.4002780.4002780.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS840840840
D min/max/mean-0.9951.471-0.017

-
Supplemental data

-
Sample components

-
Entire : Melbournevirus particle

EntireName: Melbournevirus particle
Components
  • Virus: Melbournevirus

-
Supramolecule #1: Melbournevirus

SupramoleculeName: Melbournevirus / type: virus / ID: 1 / Parent: 0 / NCBI-ID: 1560514 / Sci species name: Melbournevirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Acanthamoeba (eukaryote)
Virus shellShell ID: 1 / Name: Capsid / Diameter: 2320.0 Å / T number (triangulation number): 309

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
GridModel: R1.2/1.3 Quantifoil Micro Tools GmbH / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeJEOL 2200FS
Image recordingFilm or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.2 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm
Sample stageSpecimen holder model: JEOL / Cooling holder cryogen: NITROGEN

+
Image processing

Particle selectionNumber selected: 7005
CTF correctionSoftware - Name: EMAN2
Startup modelType of model: INSILICO MODEL
In silico model: Random initial model was generated by EMAN2 software.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 26.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 7005
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

+
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