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- PDB-5w7g: An envelope of a filamentous hyperthermophilic virus carries lipi... -

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Basic information

Entry
Database: PDB / ID: 5w7g
TitleAn envelope of a filamentous hyperthermophilic virus carries lipids in a horseshoe conformation
Components
  • DNA (253-MER)
  • ORF132
  • ORF140
KeywordsVIRUS / AFV1 / hyperthermophile / filamentous virus / A-form DNA
Function / homologyFilamentous archaeal viruses coat protein, C-terminal / helical viral capsid / DNA binding / DNA / DNA (> 10) / DNA (> 100) / Major capsid protein 1 / Major capsid protein 2
Function and homology information
Biological speciesAcidianus filamentous virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 4.5 Å
AuthorsKasson, P. / DiMaio, F. / Yu, X. / Lucas-Staat, S. / Krupovic, M. / Schouten, S. / Prangishvili, D. / Egelman, E.
Funding support United States, France, 3items
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, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 19, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 13, 2017Group: Author supporting evidence / Data collection / Category: em_software / pdbx_audit_support
Item: _em_software.name / _pdbx_audit_support.funding_organization
Revision 1.2Oct 4, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure viewerMolecule:
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Assembly

Deposited unit
A: ORF140
B: ORF132
C: ORF140
D: ORF132
E: ORF140
F: ORF132
G: ORF140
H: ORF132
I: ORF140
J: ORF132
K: ORF140
L: ORF132
M: ORF140
N: ORF132
O: ORF140
P: ORF132
Q: ORF140
R: ORF132
S: ORF140
T: ORF132
U: ORF140
V: ORF132
W: ORF140
X: ORF132
Y: ORF140
Z: ORF132
a: ORF140
b: ORF132
c: ORF140
d: ORF132
e: ORF140
f: ORF132
g: ORF140
h: ORF132
i: ORF140
j: ORF132
k: ORF140
l: ORF132
m: ORF140
n: ORF132
o: ORF140
p: ORF132
q: DNA (253-MER)
r: DNA (253-MER)


Theoretical massNumber of molelcules
Total (without water)803,34544
Polymers803,34544
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area247160 Å2
ΔGint-1451 kcal/mol
Surface area213380 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 4.6 Å / Rotation per n subunits: 38.7 °)

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Components

#1: Protein ...
ORF140


Mass: 15832.856 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 1 / References: UniProt: Q70LC6
#2: Protein ...
ORF132


Mass: 15017.159 Da / Num. of mol.: 21 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 1 / References: UniProt: Q70LC7
#3: DNA chain DNA (253-MER)


Mass: 77747.367 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Acidianus filamentous virus 1

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

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Sample preparation

ComponentName: Acidianus filamentous virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Acidianus filamentous virus 1
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 20 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
7Rosettamodel fitting
9Rosettamodel refinement
13SPIDER3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 38.7 ° / Axial rise/subunit: 4.6 Å / Axial symmetry: C1
3D reconstructionResolution: 4.5 Å / Resolution method: OTHER / Num. of particles: 119495 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL

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