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- PDB-6oj0: Cryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1) -

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Basic information

Entry
Database: PDB / ID: 6oj0
TitleCryo-EM reconstruction of Sulfolobus polyhedral virus 1 (SPV1)
Components
  • Structural protein VP4
  • Uncharacterized protein
KeywordsVIRUS / archaeal pilus / STRUCTURAL PROTEIN / icosahedral symmetry
Function / homologyicosahedral viral capsid / Capsid protein VP10 / Capsid protein VP4
Function and homology information
Biological speciesSulfolobus polyhedral virus 1
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsWang, F. / Liu, Y. / Conway, J.F. / Krupovic, M. / Prangishvili, D. / 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: 2019
Title: A packing for A-form DNA in an icosahedral virus.
Authors: Fengbin Wang / Ying Liu / Zhangli Su / Tomasz Osinski / Guilherme A P de Oliveira / James F Conway / Stefan Schouten / Mart Krupovic / David Prangishvili / Edward H Egelman /
Abstract: Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have ...Studies on viruses infecting archaea living in the most extreme environments continue to show a remarkable diversity of structures, suggesting that the sampling continues to be very sparse. We have used electron cryo-microscopy to study at 3.7-Å resolution the structure of the polyhedral virus 1 (SPV1), which was originally isolated from a hot, acidic spring in Beppu, Japan. The 2 capsid proteins with variant single jelly-roll folds form pentamers and hexamers which assemble into a = 43 icosahedral shell. In contrast to tailed icosahedral double-stranded DNA (dsDNA) viruses infecting bacteria and archaea, and herpesviruses infecting animals and humans, where naked DNA is packed under very high pressure due to the repulsion between adjacent layers of DNA, the circular dsDNA in SPV1 is fully covered with a viral protein forming a nucleoprotein filament with attractive interactions between layers. Most strikingly, we have been able to show that the DNA is in an A-form, as it is in the filamentous viruses infecting hyperthermophilic acidophiles. Previous studies have suggested that DNA is in the B-form in bacteriophages, and our study is a direct visualization of the structure of DNA in an icosahedral virus.
History
DepositionApr 10, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Derived calculations / Category: pdbx_struct_assembly_gen / pdbx_struct_oper_list
Item: _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.matrix[1][1] ..._pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[1][3] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.matrix[2][3] / _pdbx_struct_oper_list.matrix[3][1] / _pdbx_struct_oper_list.matrix[3][2] / _pdbx_struct_oper_list.matrix[3][3] / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2] / _pdbx_struct_oper_list.vector[3]
Revision 1.2Oct 23, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.3Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.4Nov 20, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
  • Imaged by Jmol
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  • Biological unit as icosahedral 23 hexamer
  • Imaged by Jmol
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  • Deposited structure unit
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • EMDB-20083
  • Imaged by Jmol
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  • Superimposition on EM map
  • EMDB-20083
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
T: Structural protein VP4
U: Structural protein VP4
V: Structural protein VP4
W: Structural protein VP4
X: Structural protein VP4
G: Structural protein VP4
n: Structural protein VP4
o: Structural protein VP4
p: Structural protein VP4
q: Structural protein VP4
r: Structural protein VP4
g: Structural protein VP4
N: Structural protein VP4
O: Structural protein VP4
P: Structural protein VP4
Q: Structural protein VP4
R: Structural protein VP4
S: Structural protein VP4
h: Structural protein VP4
i: Structural protein VP4
j: Structural protein VP4
k: Structural protein VP4
l: Structural protein VP4
m: Structural protein VP4
H: Structural protein VP4
I: Structural protein VP4
J: Structural protein VP4
K: Structural protein VP4
L: Structural protein VP4
M: Structural protein VP4
a: Structural protein VP4
b: Structural protein VP4
c: Structural protein VP4
d: Structural protein VP4
e: Structural protein VP4
f: Structural protein VP4
A: Structural protein VP4
B: Structural protein VP4
C: Structural protein VP4
D: Structural protein VP4
E: Structural protein VP4
F: Structural protein VP4
Z: Uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)835,20243
Polymers835,20243
Non-polymers00
Water00
1
T: Structural protein VP4
U: Structural protein VP4
V: Structural protein VP4
W: Structural protein VP4
X: Structural protein VP4
G: Structural protein VP4
n: Structural protein VP4
o: Structural protein VP4
p: Structural protein VP4
q: Structural protein VP4
r: Structural protein VP4
g: Structural protein VP4
N: Structural protein VP4
O: Structural protein VP4
P: Structural protein VP4
Q: Structural protein VP4
R: Structural protein VP4
S: Structural protein VP4
h: Structural protein VP4
i: Structural protein VP4
j: Structural protein VP4
k: Structural protein VP4
l: Structural protein VP4
m: Structural protein VP4
H: Structural protein VP4
I: Structural protein VP4
J: Structural protein VP4
K: Structural protein VP4
L: Structural protein VP4
M: Structural protein VP4
a: Structural protein VP4
b: Structural protein VP4
c: Structural protein VP4
d: Structural protein VP4
e: Structural protein VP4
f: Structural protein VP4
A: Structural protein VP4
B: Structural protein VP4
C: Structural protein VP4
D: Structural protein VP4
E: Structural protein VP4
F: Structural protein VP4
Z: Uncharacterized protein
x 60


Theoretical massNumber of molelcules
Total (without water)50,112,1472580
Polymers50,112,1472580
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
T: Structural protein VP4
U: Structural protein VP4
V: Structural protein VP4
W: Structural protein VP4
X: Structural protein VP4
G: Structural protein VP4
n: Structural protein VP4
o: Structural protein VP4
p: Structural protein VP4
q: Structural protein VP4
r: Structural protein VP4
g: Structural protein VP4
N: Structural protein VP4
O: Structural protein VP4
P: Structural protein VP4
Q: Structural protein VP4
R: Structural protein VP4
S: Structural protein VP4
h: Structural protein VP4
i: Structural protein VP4
j: Structural protein VP4
k: Structural protein VP4
l: Structural protein VP4
m: Structural protein VP4
H: Structural protein VP4
I: Structural protein VP4
J: Structural protein VP4
K: Structural protein VP4
L: Structural protein VP4
M: Structural protein VP4
a: Structural protein VP4
b: Structural protein VP4
c: Structural protein VP4
d: Structural protein VP4
e: Structural protein VP4
f: Structural protein VP4
A: Structural protein VP4
B: Structural protein VP4
C: Structural protein VP4
D: Structural protein VP4
E: Structural protein VP4
F: Structural protein VP4
Z: Uncharacterized protein
x 5


  • icosahedral pentamer
  • 4.18 MDa, 215 polymers
Theoretical massNumber of molelcules
Total (without water)4,176,012215
Polymers4,176,012215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
T: Structural protein VP4
U: Structural protein VP4
V: Structural protein VP4
W: Structural protein VP4
X: Structural protein VP4
G: Structural protein VP4
n: Structural protein VP4
o: Structural protein VP4
p: Structural protein VP4
q: Structural protein VP4
r: Structural protein VP4
g: Structural protein VP4
N: Structural protein VP4
O: Structural protein VP4
P: Structural protein VP4
Q: Structural protein VP4
R: Structural protein VP4
S: Structural protein VP4
h: Structural protein VP4
i: Structural protein VP4
j: Structural protein VP4
k: Structural protein VP4
l: Structural protein VP4
m: Structural protein VP4
H: Structural protein VP4
I: Structural protein VP4
J: Structural protein VP4
K: Structural protein VP4
L: Structural protein VP4
M: Structural protein VP4
a: Structural protein VP4
b: Structural protein VP4
c: Structural protein VP4
d: Structural protein VP4
e: Structural protein VP4
f: Structural protein VP4
A: Structural protein VP4
B: Structural protein VP4
C: Structural protein VP4
D: Structural protein VP4
E: Structural protein VP4
F: Structural protein VP4
Z: Uncharacterized protein
x 6


  • icosahedral 23 hexamer
  • 5.01 MDa, 258 polymers
Theoretical massNumber of molelcules
Total (without water)5,011,215258
Polymers5,011,215258
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein ...
Structural protein VP4


Mass: 19394.885 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Source: (natural) Sulfolobus polyhedral virus 1 / References: UniProt: A0A1W6I187
#2: Protein Uncharacterized protein


Mass: 20617.277 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sulfolobus polyhedral virus 1 / References: UniProt: A0A1W6I162
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Sulfolobus spindle-shaped virus 1 / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Sulfolobus spindle-shaped virus 1
Details of virusEmpty: NO / Enveloped: YES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Sulfolobus sp. S38A
Buffer solutionpH: 4
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: 20 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.14_3260: / Classification: refinement
EM softwareName: RELION / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.7 Å / Resolution method: OTHER / Num. of particles: 19092 / Details: d99, model:map FSC (0.38), map:map FSC (0.143) / Symmetry type: POINT

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