[English] 日本語
Yorodumi
- EMDB-3857: Structure of Aeropyrum pernix bacilliform virus 1 APBV1 helical capsid -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-3857
TitleStructure of Aeropyrum pernix bacilliform virus 1 APBV1 helical capsid
Map dataAPBV1 helical capsid
Sample
  • Virus: Aeropyrum pernix bacilliform virus 1
    • Protein or peptide: Major virion protein
Function / homologymembrane => GO:0016020 / Major virion protein
Function and homology information
Biological speciesisolate -/Japan/Tanaka/2005 (virus) / Aeropyrum pernix bacilliform virus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHuiskonen JT / Ptchelkine D / Gillum A
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust203141/Z/16/Z United Kingdom
Wellcome Trust093305/Z/10/Z United Kingdom
Wellcome Trust060208/Z/00/Z United Kingdom
European Research Council649053 United Kingdom
CitationJournal: Nat Commun / Year: 2017
Title: Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging.
Authors: Denis Ptchelkine / Ashley Gillum / Tomohiro Mochizuki / Soizick Lucas-Staat / Ying Liu / Mart Krupovic / Simon E V Phillips / David Prangishvili / Juha T Huiskonen /
Abstract: Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome ...Archaeal viruses have evolved to infect hosts often thriving in extreme conditions such as high temperatures. However, there is a paucity of information on archaeal virion structures, genome packaging, and determinants of temperature resistance. The rod-shaped virus APBV1 (Aeropyrum pernix bacilliform virus 1) is among the most thermostable viruses known; it infects a hyperthermophile Aeropyrum pernix, which grows optimally at 90 °C. Here we report the structure of APBV1, determined by cryo-electron microscopy at near-atomic resolution. Tight packing of the major virion glycoprotein (VP1) is ensured by extended hydrophobic interfaces, and likely contributes to the extreme thermostability of the helical capsid. The double-stranded DNA is tightly packed in the capsid as a left-handed superhelix and held in place by the interactions with positively charged residues of VP1. The assembly is closed by specific capping structures at either end, which we propose to play a role in DNA packing and delivery.
History
DepositionSep 6, 2017-
Header (metadata) releaseNov 8, 2017-
Map releaseNov 22, 2017-
UpdateNov 25, 2020-
Current statusNov 25, 2020Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5oxe
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5oxe
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3857.png

Downloads & links

-
Map

FileDownload / File: emd_3857.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAPBV1 helical capsid
Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.03 / Movie #1: 0.03
Minimum - Maximum-0.11308209 - 0.18221602
Average (Standard dev.)-0.00078583346 (±0.015131986)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z243.000243.000243.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-0.1130.182-0.001

-
Supplemental data

-
Mask #1

Fileemd_3857_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: APBV1 helical capsid, half map 1

Fileemd_3857_half_map_1.map
AnnotationAPBV1 helical capsid, half map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: APBV1 helical capsid, half map 2

Fileemd_3857_half_map_2.map
AnnotationAPBV1 helical capsid, half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Aeropyrum pernix bacilliform virus 1

EntireName: Aeropyrum pernix bacilliform virus 1
Components
  • Virus: Aeropyrum pernix bacilliform virus 1
    • Protein or peptide: Major virion protein

-
Supramolecule #1: Aeropyrum pernix bacilliform virus 1

SupramoleculeName: Aeropyrum pernix bacilliform virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 700542 / Sci species name: Aeropyrum pernix bacilliform virus 1 / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Aeropyrum pernix (archaea)

-
Macromolecule #1: Major virion protein

MacromoleculeName: Major virion protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: isolate -/Japan/Tanaka/2005 (virus)
Molecular weightTheoretical: 8.272858 KDa
SequenceString:
MAPKATLVKK FKGLAVGVGA LLAAPPIMGL ASYAVNGISS YLSITINSTT YDFAPLAQAV MVFGGIGLVA YGLHRILGRG L

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

-
Sample preparation

BufferpH: 7 / Details: distilled water
VitrificationCryogen name: ETHANE-PROPANE

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm
Specialist opticsEnergy filter - Name: K2 Summit / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: COUNTING / Average exposure time: 0.2 sec. / Average electron dose: 1.0 e/Å2
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

Particle selectionNumber selected: 169316
Details: Overlapping segments extracted from helical particles
CTF correctionSoftware - Name: CTFFIND (ver. 3)
Startup modelType of model: OTHER
Details: Helical reconstruction generated by inverse Fourier-Bessel transform of layer line data
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPRING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPRING
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPRING / Number images used: 94645
FSC plot (resolution estimation)

-
Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-5oxe:
Structure of major capsid protein VP1 of Aeropyrum pernix bacilliform virus 1 APBV1

+
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