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- EMDB-3857: Structure of Aeropyrum pernix bacilliform virus 1 APBV1 helical capsid -

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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
Keywordsarchaeal virus / thermophile / capsid / helical / VIRUS
Function / homologymembrane / Major virion protein
Function and homology information
Biological speciesAeropyrum 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 Trust060208/Z/00/Z United Kingdom
Wellcome Trust093305/Z/10/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-
UpdateMay 15, 2024-
Current statusMay 15, 2024Processing site: PDBe / Status: Released

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Structure visualization

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

emd_3857.png

Downloads & links

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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
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å		1.35 Å/pix.
x 180 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density

Histogram

Histogram (log scale)
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

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Supplemental data

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Mask #1

Fileemd_3857_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)

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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)

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Sample components

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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

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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)

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Macromolecule #1: Major virion protein

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

UniProtKB: Major virion protein

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statehelical array

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Sample preparation

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

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Electron microscopy

MicroscopeFEI POLARA 300
Specialist opticsEnergy filter - Name: K2 Summit / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV
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
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 FIELD / Cs: 2.0 mm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 169316
Details: Overlapping segments extracted from helical particles
Startup modelType of model: OTHER
Details: Helical reconstruction generated by inverse Fourier-Bessel transform of layer line data
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
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: SPRING
Final angle assignmentType: PROJECTION MATCHING / Software - Name: SPRING
FSC plot (resolution estimation)

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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

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