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- EMDB-8780: An envelope of a filamentous hyperthermophilic virus carries lipi... -

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Basic information

Entry
Database: EMDB / ID: EMD-8780
TitleAn envelope of a filamentous hyperthermophilic virus carries lipids in a horseshoe conformation
Map dataenvelope of a filamentous hyperthermophilic virus
Sample
  • Virus: Acidianus filamentous virus 1
    • Protein or peptide: ORF140
    • Protein or peptide: ORF132
    • DNA: DNA (253-MER)
KeywordsAFV1 / hyperthermophile / filamentous virus / A-form DNA / VIRUS
Function / homologyFilamentous archaeal viruses coat protein, C-terminal / helical viral capsid / DNA binding / Major capsid protein 1 / Major capsid protein 2
Function and homology information
Biological speciesAcidianus filamentous virus 1
Methodhelical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKasson P / DiMaio F
Funding support United States, France, 3 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM035269 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM098304 United States
French National Research AgencyANR-13-BSV3-0017-01 France
CitationJournal: Elife / Year: 2017
Title: Model for a novel membrane envelope in a filamentous hyperthermophilic virus.
Authors: Peter Kasson / Frank DiMaio / Xiong Yu / Soizick Lucas-Staat / Mart Krupovic / Stefan Schouten / David Prangishvili / Edward H Egelman /
Abstract: Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers ...Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of , are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped 'horseshoe' conformation. We hypothesize that this unusual viral envelope structure results from the extreme curvature of the viral capsid, as 'horseshoe' lipid conformations favor such curvature and host membrane lipids that permit horseshoe conformations are selectively recruited into the viral envelope. The unusual envelope found in AFV1 also has many implications for biotechnology, since this membrane can survive the most aggressive conditions involving extremes of temperature and pH.
History
DepositionJun 19, 2017-
Header (metadata) releaseJul 19, 2017-
Map releaseJul 19, 2017-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5w7g
  • Surface level: 0.4
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5w7g
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8780.png

Downloads & links

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Map

FileDownload / File: emd_8780.map.gz / Format: CCP4 / Size: 28.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationenvelope of a filamentous hyperthermophilic virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 200 pix.
= 210. Å		1.05 Å/pix.
x 192 pix.
= 201.6 Å		1.05 Å/pix.
x 192 pix.
= 201.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 1.05 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.4 / Movie #1: 0.4
Minimum - Maximum-0.44741467 - 0.9573618
Average (Standard dev.)0.058518816 (±0.14860396)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192200
Spacing192192200
CellA: 201.59999 Å / B: 201.59999 Å / C: 209.99998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z192192200
origin x/y/z0.0000.0000.000
length x/y/z201.600201.600210.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192200
D min/max/mean-0.4470.9570.059

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Supplemental data

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Sample components

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Entire : Acidianus filamentous virus 1

EntireName: Acidianus filamentous virus 1
Components
  • Virus: Acidianus filamentous virus 1
    • Protein or peptide: ORF140
    • Protein or peptide: ORF132
    • DNA: DNA (253-MER)

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Supramolecule #1: Acidianus filamentous virus 1

SupramoleculeName: Acidianus filamentous virus 1 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 235266 / Sci species name: Acidianus filamentous virus 1 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No

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Macromolecule #1: ORF140

MacromoleculeName: ORF140 / type: protein_or_peptide / ID: 1 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Acidianus filamentous virus 1
Molecular weightTheoretical: 15.832856 KDa
SequenceString:
MAKLNRKLRQ DSTDRYKTKL YLWRNLGGLI PEDMAISVTE SITADWKQYN DMMSKVRNET LDILKTNKVA TEDYIGYIAF AEELAHQVW KNKNSSPDPN TANEASKTDL ESKYSDVYGL DVTVLDAIYN AVIPIIMGGG S

UniProtKB: Major capsid protein 1

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Macromolecule #2: ORF132

MacromoleculeName: ORF132 / type: protein_or_peptide / ID: 2 / Number of copies: 21 / Enantiomer: LEVO
Source (natural)Organism: Acidianus filamentous virus 1
Molecular weightTheoretical: 15.017159 KDa
SequenceString:
MVNKKYRQDS KDRYQYKQYI YRSIGGIVPP EMAETVTANQ TAQWEAGFTP YHKLRLAIKE ICKTDGIPNI KWGMYIAFGE KLLKSYLKM KAGSASSDMI AEYINNAISA FSSRTGISQE TAQKIADFIT SNY

UniProtKB: Major capsid protein 2

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Macromolecule #3: DNA (253-MER)

MacromoleculeName: DNA (253-MER) / type: dna / ID: 3 / Number of copies: 2 / Classification: DNA
Source (natural)Organism: Acidianus filamentous virus 1
Molecular weightTheoretical: 77.747367 KDa
SequenceString: (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT) ...String:
(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT)(DA) (DT) (DA)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DT)(DA)(DT)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 6
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 4.6 Å
Applied symmetry - Helical parameters - Δ&Phi: 38.7 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.5 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 119495
Startup modelType of model: OTHER
Final angle assignmentType: NOT APPLICABLE

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