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- PDB-3j9x: A Virus that Infects a Hyperthermophile Encapsidates A-Form DNA -

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Basic information

Entry
Database: PDB / ID: 3j9x
TitleA Virus that Infects a Hyperthermophile Encapsidates A-Form DNA
Components
  • DNA
  • coat protein
KeywordsVIRUS / archaeal virus / helical symmetry
Function / homology
Function and homology information


helical viral capsid / DNA binding
Similarity search - Function
Sulfolobus virus, coat protein, C-terminal / Sulfolobus virus coat protein C terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #800 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Major capsid protein
Similarity search - Component
Biological speciesSulfolobus islandicus rod-shaped virus 2
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsDiMaio, F. / Yu, X. / Rensen, E. / Krupovic, M. / Prangishvili, D. / Egelman, E.
CitationJournal: Science / Year: 2015
Title: Virology. A virus that infects a hyperthermophile encapsidates A-form DNA.
Authors: Frank DiMaio / Xiong Yu / Elena Rensen / Mart Krupovic / David Prangishvili / Edward H Egelman /
Abstract: Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus ...Extremophiles, microorganisms thriving in extreme environmental conditions, must have proteins and nucleic acids that are stable at extremes of temperature and pH. The nonenveloped, rod-shaped virus SIRV2 (Sulfolobus islandicus rod-shaped virus 2) infects the hyperthermophilic acidophile Sulfolobus islandicus, which lives at 80°C and pH 3. We have used cryo-electron microscopy to generate a three-dimensional reconstruction of the SIRV2 virion at ~4 angstrom resolution, which revealed a previously unknown form of virion organization. Although almost half of the capsid protein is unstructured in solution, this unstructured region folds in the virion into a single extended α helix that wraps around the DNA. The DNA is entirely in the A-form, which suggests a common mechanism with bacterial spores for protecting DNA in the most adverse environments.
History
DepositionMar 21, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 18, 2018Group: Author supporting evidence / Data collection / Category: em_single_particle_entity / em_software / Item: _em_software.image_processing_id
Revision 1.2Feb 21, 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: coat protein
B: coat protein
C: coat protein
D: coat protein
E: coat protein
F: coat protein
G: coat protein
H: coat protein
I: coat protein
J: coat protein
K: coat protein
L: coat protein
M: coat protein
N: coat protein
O: coat protein
P: coat protein
Q: coat protein
R: coat protein
S: coat protein
T: coat protein
U: coat protein
V: coat protein
W: coat protein
X: coat protein
Y: coat protein
Z: coat protein
a: coat protein
b: coat protein
c: coat protein
d: coat protein
e: coat protein
f: coat protein
g: coat protein
h: coat protein
i: coat protein
j: coat protein
k: coat protein
l: coat protein
m: coat protein
n: coat protein
o: coat protein
p: coat protein
q: coat protein
r: coat protein
s: coat protein
t: coat protein
u: coat protein
v: coat protein
w: coat protein
x: coat protein
y: coat protein
z: coat protein
1: coat protein
2: coat protein
3: coat protein
4: coat protein
5: coat protein
6: coat protein
7: DNA
8: DNA


Theoretical massNumber of molelcules
Total (without water)1,012,87260
Polymers1,012,87260
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
SymmetryHelical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 30 / Rise per n subunits: 2.9 Å / Rotation per n subunits: 24.5 °)
DetailsThe helical parameters generate the capsid filament from chains A and B.

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Components

#1: Protein ...
coat protein


Mass: 13760.465 Da / Num. of mol.: 58 / Source method: isolated from a natural source / Source: (natural) Sulfolobus islandicus rod-shaped virus 2 / References: UniProt: Q8V9P2
#2: DNA chain DNA


Mass: 107382.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sulfolobus islandicus rod-shaped virus 2

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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: Sulfolobus islandicus rod-shaped virus 2 / Type: VIRUS / Synonym: SIRV2
Details of virusEmpty: NO / Enveloped: NO / Host category: ARCHAEA / Isolate: SPECIES / Type: VIRION
Natural hostOrganism: Sulfolobus islandicus
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Details: Plunged into liquid ethane (FEI VITROBOT MARK IV).

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Sep 19, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm
Specimen holderSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 20 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)
Image scansNum. digital images: 437
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM softwareName: SPIDER / Category: 3D reconstruction
CTF correctionDetails: multiply images by CTF, divide reconstruction by sum of CTF**2
Helical symmertyAngular rotation/subunit: 24.5 ° / Axial rise/subunit: 2.9 Å / Axial symmetry: C1
3D reconstructionMethod: IHRSR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Nominal pixel size: 1.05 Å / Actual pixel size: 1.05 Å / Details: (Helical Details: IHRSR) / Symmetry type: HELICAL
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms56434 14268 0 0 70702

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