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- PDB-7xgz: Cryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid... -

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Basic information

Entry
Database: PDB / ID: 7xgz
TitleCryo-EM structure of the T=4 lake sinai virus 2 virus-like capsid at pH 7.5
ComponentsCapsid protein alpha
KeywordsVIRUS LIKE PARTICLE
Function / homologyvirion component / Viral coat protein subunit / Capsid protein alpha
Function and homology information
Biological speciesLake Sinai virus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.24 Å
AuthorsChen, N.C. / Wang, C.H. / Chen, C.J. / Yoshimura, M. / Guan, H.H. / Chuankhayan, P. / Lin, C.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, Taiwan) Taiwan
CitationJournal: Nat Commun / Year: 2023
Title: Structures of honeybee-infecting Lake Sinai virus reveal domain functions and capsid assembly with dynamic motions
Authors: Chen, N.C. / Wang, C.H. / Yoshimura, M. / Yeh, Y.Q. / Guan, H.H. / Chuankhayan, P. / Lin, C.C. / Lin, P.J. / Huang, Y.C. / Wakatsuki, S. / Ho, M.C. / Chen, C.J.
History
DepositionApr 7, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 8, 2023Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title
Revision 1.2Jul 3, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond / em_admin / Item: _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
D: Capsid protein alpha


Theoretical massNumber of molelcules
Total (without water)229,3774
Polymers229,3774
Non-polymers00
Water00
1
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
D: Capsid protein alpha
x 60


Theoretical massNumber of molelcules
Total (without water)13,762,634240
Polymers13,762,634240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
D: Capsid protein alpha
x 5


  • icosahedral pentamer
  • Evidence: gel filtration
  • 1.15 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,146,88620
Polymers1,146,88620
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein alpha
B: Capsid protein alpha
C: Capsid protein alpha
D: Capsid protein alpha
x 6


  • icosahedral 23 hexamer
  • Evidence: gel filtration
  • 1.38 MDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)1,376,26324
Polymers1,376,26324
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
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein
Capsid protein alpha


Mass: 57344.309 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lake Sinai virus 2 / Production host: Escherichia coli (E. coli) / References: UniProt: F8TEV4

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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: Lake Sinai virus 2 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Lake Sinai virus 2
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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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 / Nominal defocus max: 2720 nm / Nominal defocus min: 250 nm
Image recordingElectron dose: 46 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM software
IDNameCategory
4CTFFINDCTF correction
10cisTEMinitial Euler assignment
11cryoSPARCfinal Euler assignment
12cryoSPARCclassification
CTF correctionType: PHASE FLIPPING ONLY
Particle selectionNum. of particles selected: 30227
3D reconstructionResolution: 3.24 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30227 / Symmetry type: POINT

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