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- PDB-6v7b: Cryo-EM reconstruction of Pyrobaculum filamentous virus 2 (PFV2) -

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Basic information

Entry
Database: PDB / ID: 6v7b
TitleCryo-EM reconstruction of Pyrobaculum filamentous virus 2 (PFV2)
Components
  • (A-DNA) x 2
  • Structural protein VP1Structure
  • Structural protein VP2Structure
KeywordsVIRUS / helical symmetry / archaeal pilus / STRUCTURAL PROTEIN
Function / homologyDNA / DNA (> 10) / DNA (> 100) / Structural protein VP1 / Structural protein VP2
Function and homology information
Biological speciesPyrobaculum filamentous virus 1
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang, F. / Baquero, D.P. / Su, Z. / Prangishvili, D. / Krupovic, M. / Egelman, E.H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122510 United States
CitationJournal: Virus Evol / Year: 2020
Title: Structure of a filamentous virus uncovers familial ties within the archaeal virosphere.
Authors: Fengbin Wang / Diana P Baquero / Zhangli Su / Tomasz Osinski / David Prangishvili / Edward H Egelman / Mart Krupovic /
Abstract: Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to ...Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to viruses of bacteria and eukaryotes. Tristromaviruses, which build enveloped filamentous virions and infect hyperthermophilic neutrophiles of the order Thermoproteales, represent one such enigmatic virus families. They do not share genes with viruses from other families and have been believed to represent an evolutionarily independent virus lineage. A cryo-electron microscopic reconstruction of the tristromavirus Pyrobaculum filamentous virus 2 at 3.4 Å resolution shows that the virion is constructed from two paralogous major capsid proteins (MCP) which transform the linear dsDNA genome of the virus into A-form by tightly wrapping around it. Unexpectedly, the two MCP are homologous to the capsid proteins of other filamentous archaeal viruses, uncovering a deep evolutionary relationship within the archaeal virosphere.
History
DepositionDec 8, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2May 20, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.page_first ..._citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

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  • Deposited structure unit
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Assembly

Deposited unit
1: A-DNA
2: A-DNA
A: Structural protein VP1
B: Structural protein VP1
C: Structural protein VP1
D: Structural protein VP1
E: Structural protein VP1
F: Structural protein VP1
G: Structural protein VP1
H: Structural protein VP1
I: Structural protein VP1
J: Structural protein VP1
K: Structural protein VP1
L: Structural protein VP1
M: Structural protein VP1
N: Structural protein VP1
O: Structural protein VP1
P: Structural protein VP1
Q: Structural protein VP1
R: Structural protein VP1
S: Structural protein VP1
T: Structural protein VP1
U: Structural protein VP1
V: Structural protein VP1
W: Structural protein VP1
a: Structural protein VP2
b: Structural protein VP2
c: Structural protein VP2
d: Structural protein VP2
e: Structural protein VP2
f: Structural protein VP2
g: Structural protein VP2
h: Structural protein VP2
i: Structural protein VP2
j: Structural protein VP2
k: Structural protein VP2
l: Structural protein VP2
m: Structural protein VP2
n: Structural protein VP2
o: Structural protein VP2
p: Structural protein VP2
q: Structural protein VP2
r: Structural protein VP2
s: Structural protein VP2
t: Structural protein VP2
u: Structural protein VP2
v: Structural protein VP2
w: Structural protein VP2


Theoretical massNumber of molelcules
Total (without water)896,52848
Polymers896,52848
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy, helical filament was observed by negative staining and Cryo-EM
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area316570 Å2
ΔGint-1463 kcal/mol
Surface area240570 Å2
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 23 / Rise per n subunits: 2.864 Å / Rotation per n subunits: 22.9482 °)

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Components

#1: DNA chain A-DNA /


Mass: 99669.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1
#2: DNA chain A-DNA /


Mass: 99660.539 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1
#3: Protein ...
Structural protein VP1 / Structure


Mass: 14986.418 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 / References: UniProt: A0A140F3K6
#4: Protein ...
Structural protein VP2 / Structure


Mass: 15326.556 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Source: (natural) Pyrobaculum filamentous virus 1 / References: UniProt: A0A140F3K7

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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: Pyrobaculum filamentous virus 2 / Type: COMPLEX / Entity ID: all / Source: NATURAL
Source (natural)Organism: Pyrobaculum filamentous virus 1
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 90 %

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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 recordingAverage exposure time: 2 sec. / Electron dose: 44 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM software
IDNameCategory
1EMAN2particle selection
2EPUimage acquisition
4GctfCTF correction
12SPIDER3D reconstruction
13RELION3D reconstruction
14Rosettamodel refinement
15PHENIXmodel refinement
16Cootmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 22.9482 ° / Axial rise/subunit: 2.864 Å / Axial symmetry: C1
3D reconstructionResolution: 3.4 Å / Resolution method: OTHER / Num. of particles: 186576 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL

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