[English] 日本語
Yorodumi
- EMDB-1351: Structure and host cell interaction of SH1, a membrane-containing... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-1351
TitleStructure and host cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus
Map dataCryoEM reconstruction of SH1 subviral particle VP36-.
Sample
  • Sample: SH1 subviral particle VP36-
  • Virus: Haloarcula phage SH1 (virus)
Biological speciesHaloarcula phage SH1 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsJaalinoja HT / Roine E / Kivela H / Butcher SJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Structure and host-cell interaction of SH1, a membrane-containing, halophilic euryarchaeal virus.
Authors: Harri T Jäälinoja / Elina Roine / Pasi Laurinmäki / Hanna M Kivelä / Dennis H Bamford / Sarah J Butcher /
Abstract: The Archaea, and the viruses that infect them, are the least well understood of all of the three domains of life. They often grow in extreme conditions such as hypersaline lakes and sulfuric hot ...The Archaea, and the viruses that infect them, are the least well understood of all of the three domains of life. They often grow in extreme conditions such as hypersaline lakes and sulfuric hot springs. Only rare glimpses have been gained into the structures of archaeal viruses. Here, we report the subnanometer resolution structure of a recently isolated, hypersalinic, membrane-containing, euryarchaeal virus, SH1, in which different viral proteins can be localized. The results indicate that SH1 has a complex capsid formed from single beta-barrels, an important missing link in hypotheses on viral capsid protein evolution. Unusual, symmetry-mismatched spikes seem to play a role in host adsorption. They are connected to highly organized membrane proteins providing a platform for capsid assembly and potential machinery for host infection.
History
DepositionApr 2, 2007-
Header (metadata) releaseApr 2, 2007-
Map releaseMay 17, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5000
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 5000
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_1351.map.gz / Format: CCP4 / Size: 139 MB / Type: IMAGE STORED AS SIGNED INTEGER (2 BYTES)
AnnotationCryoEM reconstruction of SH1 subviral particle VP36-.
Voxel sizeX=Y=Z: 2.8 Å
Density
Contour Level1: 5640.0 / Movie #1: 5000
Minimum - Maximum-15891.0 - 32443.0
Average (Standard dev.)304.646000000000015 (±3311.019999999999982)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions421421421
Spacing421421421
CellA=B=C: 1178.8 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z2.82.82.8
M x/y/z421421421
origin x/y/z0.0000.0000.000
length x/y/z1178.8001178.8001178.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS421421421
D min/max/mean-15891.00032443.000304.646

-
Supplemental data

-
Sample components

-
Entire : SH1 subviral particle VP36-

EntireName: SH1 subviral particle VP36-
Components
  • Sample: SH1 subviral particle VP36-
  • Virus: Haloarcula phage SH1 (virus)

-
Supramolecule #1000: SH1 subviral particle VP36-

SupramoleculeName: SH1 subviral particle VP36- / type: sample / ID: 1000 / Number unique components: 1

-
Supramolecule #1: Haloarcula phage SH1

SupramoleculeName: Haloarcula phage SH1 / type: virus / ID: 1 / Name.synonym: SH1 subviral particle VP36- / NCBI-ID: 326574 / Sci species name: Haloarcula phage SH1 / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: SH1 subviral particle VP36-
Host (natural)Organism: Haloarcula hispanica (Halophile) / synonym: ARCHAEA
Virus shellShell ID: 1 / Name: capsid / Diameter: 800 Å / T number (triangulation number): 28

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2 / Details: 40 mM Tris-HCl pH 7.2, 0.75 M Na2SO4, 40 mM MgSO4
GridDetails: 400 mesh copper grid, Quantifoil R2/2 holey
VitrificationCryogen name: ETHANE / Chamber temperature: 90 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: EMBL design
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding 3 microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot off excess buffer, sufficient to leave a thin layer on the grid. The filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed in liquid nitrogen for later use in the microscope.

-
Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49300 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.484 µm / Nominal defocus min: 0.733 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 90 K / Max: 94 K / Average: 93 K
DetailsLow dose conditions.
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 58
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: Each particle, wiener factor 0.2
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: pft2, em3dr2, POR, P3DR / Number images used: 985

+
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