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- PDB-6wq0: Cryo-EM of the S. solfataricus rod-shaped virus, SSRV1 -

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Basic information

Entry
Database: PDB / ID: 6wq0
TitleCryo-EM of the S. solfataricus rod-shaped virus, SSRV1
Components
  • (DNA (301-MER)) x 2
  • Structural protein
KeywordsVIRUS / helical symmetry / archaeal virus / rod-like virus / structural protein
Function / homologyDNA / DNA (> 10) / DNA (> 100)
Function and homology information
Biological speciesunclassified Rudivirus
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsWang, F. / Baquero, D.P. / Beltran, L.C. / 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: Proc Natl Acad Sci U S A / Year: 2020
Title: Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments.
Authors: Fengbin Wang / Diana P Baquero / Leticia C Beltran / Zhangli Su / Tomasz Osinski / Weili Zheng / David Prangishvili / Mart Krupovic / Edward H Egelman /
Abstract: Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) ...Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homodimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homodimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenveloped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution.
History
DepositionApr 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 6, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Assembly

Deposited unit
7: DNA (301-MER)
8: DNA (301-MER)
A: Structural protein
B: Structural protein
C: Structural protein
D: Structural protein
E: Structural protein
F: Structural protein
G: Structural protein
H: Structural protein
I: Structural protein
J: Structural protein
K: Structural protein
L: Structural protein
M: Structural protein
N: Structural protein
O: Structural protein
P: Structural protein
Q: Structural protein
R: Structural protein
S: Structural protein
T: Structural protein
U: Structural protein
V: Structural protein
W: Structural protein
a: Structural protein
b: Structural protein
c: Structural protein
d: Structural protein
e: Structural protein
f: Structural protein
g: Structural protein
h: Structural protein
i: Structural protein
j: Structural protein
k: Structural protein
l: Structural protein
m: Structural protein
n: Structural protein
o: Structural protein
p: Structural protein
q: Structural protein
r: Structural protein
s: Structural protein
t: Structural protein
u: Structural protein
v: Structural protein
w: Structural protein


Theoretical massNumber of molelcules
Total (without water)839,27448
Polymers839,27448
Non-polymers00
Water00
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 area370700 Å2
ΔGint-2578 kcal/mol
Surface area185600 Å2

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Components

#1: DNA chain DNA (301-MER)


Mass: 92878.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus
Plasmid details: It is rod-like virus purified from a S. solfataricus strain
#2: DNA chain DNA (301-MER)


Mass: 92869.141 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus
#3: Protein ...
Structural protein


Mass: 14207.113 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Source: (natural) unclassified Rudivirus

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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: S. solfataricus rod-shaped virus, SSRV1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: unclassified Rudivirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Saccharolobus solfataricus
Buffer solutionpH: 6
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen name: ETHANE

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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 FIELD
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.15.2_3472: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 24.53 ° / Axial rise/subunit: 2.94 Å / Axial symmetry: D1
3D reconstructionResolution: 2.8 Å / Resolution method: OTHER / Num. of particles: 470000 / Details: MODEL:MAP FSC, D99, MAP:MAP FSC / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00759982
ELECTRON MICROSCOPYf_angle_d0.69284291
ELECTRON MICROSCOPYf_dihedral_angle_d7.96333200
ELECTRON MICROSCOPYf_chiral_restr0.0459584
ELECTRON MICROSCOPYf_plane_restr0.0078744

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