[English] 日本語
Yorodumi
- EMDB-20746: Low pH and High Temperature-Treated Samba Virus -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-20746
TitleLow pH and High Temperature-Treated Samba Virus
Map dataLow pH and high temperature-treated Samba virus particle.
Sample
  • Virus: Samba virus
Biological speciesSamba virus
Methodelectron tomography / cryo EM
AuthorsSchrad JR / Parent KN
Funding support United States, 5 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical SciencesU24GM116789-03 United States
AAAS Marion Mason Milligan Award for Women in the Chemical Sciences United States
National Institutes of Health/National Human Genome Research InstituteGM110185 United States
NVIDIA GPU grant program United States
Burroughs Wellcome Fund Investigators in the Pathogenicity of Disease United States
CitationJournal: Cell / Year: 2020
Title: Structural and Proteomic Characterization of the Initiation of Giant Virus Infection.
Authors: Jason R Schrad / Jônatas S Abrahão / Juliana R Cortines / Kristin N Parent /
Abstract: Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. ...Since their discovery, giant viruses have expanded our understanding of the principles of virology. Due to their gargantuan size and complexity, little is known about the life cycles of these viruses. To answer outstanding questions regarding giant virus infection mechanisms, we set out to determine biomolecular conditions that promote giant virus genome release. We generated four infection intermediates in Samba virus (Mimivirus genus, lineage A) as visualized by cryoelectron microscopy (cryo-EM), cryoelectron tomography (cryo-ET), and scanning electron microscopy (SEM). Each of these four intermediates reflects similar morphology to a stage that occurs in vivo. We show that these genome release stages are conserved in other mimiviruses. Finally, we identified proteins that are released from Samba and newly discovered Tupanvirus through differential mass spectrometry. Our work revealed the molecular forces that trigger infection are conserved among disparate giant viruses. This study is also the first to identify specific proteins released during the initial stages of giant virus infection.
History
DepositionSep 20, 2019-
Header (metadata) releaseOct 2, 2019-
Map releaseMay 13, 2020-
UpdateJun 10, 2020-
Current statusJun 10, 2020Processing site: RCSB / Status: Released

-
Structure visualization

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

emd_20746.png

Downloads & links

-
Map

FileDownload / File: emd_20746.map.gz / Format: CCP4 / Size: 206.5 MB / Type: IMAGE STORED AS SIGNED BYTE
AnnotationLow pH and high temperature-treated Samba virus particle.
Voxel sizeX=Y=Z: 4.2 Å
Density
Minimum - Maximum-128 - 127
Average (Standard dev.)6.4591455 (±13.033827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-199-137140
Dimensions744708411
Spacing708744411
CellA: 2973.5999 Å / B: 3124.7998 Å / C: 1726.2 Å
α=β=γ: 90.0 °

CCP4 map header:

modeenvelope stored as signed bytes (from -128 lowest to 127 highest)
Å/pix. X/Y/Z4.24.24.2
M x/y/z708744411
origin x/y/z0.0000.0000.000
length x/y/z2973.6003124.8001726.200
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-137-199140
NC/NR/NS708744411
D min/max/mean-128.000127.0006.459

-
Supplemental data

-
Sample components

-
Entire : Samba virus

EntireName: Samba virus
Components
  • Virus: Samba virus

-
Supramolecule #1: Samba virus

SupramoleculeName: Samba virus / type: virus / ID: 1 / Parent: 0
Details: Low pH and high temperature-treated Samba virus particle.
NCBI-ID: 1461100 / Sci species name: Samba virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: Yes
Host (natural)Organism: Acanthamoeba castellanii (eukaryote) / Strain: Neff

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation stateparticle

-
Sample preparation

BufferpH: 2 / Component - Concentration: 20.0 mM / Component - Formula: NaPO4 / Component - Name: sodium phosphate
GridModel: Quantifoil R2/2 / Material: COPPER / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Atmosphere: AIR / Details: Fischione model 1020
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
DetailsLow pH and high temperature-treated Samba virus particle. ~1x10^9 particles per mL
SectioningOther: NO SECTIONING
Fiducial markerManufacturer: Aldrich / Diameter: 10 nm

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 70.0 K / Max: 70.0 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average exposure time: 5.0 sec. / Average electron dose: 2.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 33000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

DetailsMotionCor2 to align frames
Final reconstructionAlgorithm: SIMULTANEOUS ITERATIVE (SIRT) / Software - Name: IMOD (ver. 4.7.5) / Number images used: 51

+
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