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- PDB-6edj: Cryo-EM structure of Woodchuck hepatitis virus capsid -

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Basic information

Entry
Database: PDB / ID: 6edj
TitleCryo-EM structure of Woodchuck hepatitis virus capsid
ComponentsExternal core antigen
KeywordsVIRUS LIKE PARTICLE / WHV / Capsid structure
Function / homology
Function and homology information


microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / evasion or tolerance by virus of host immune response / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / host cell nucleus / structural molecule activity / RNA binding ...microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / evasion or tolerance by virus of host immune response / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / host cell nucleus / structural molecule activity / RNA binding / DNA binding / extracellular region
Hepatitis core antigen / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Hepatitis B virus, capsid N-terminal / Viral capsid core domain supefamily, Hepatitis B virus
External core antigen
Specimen sourceWoodchuck hepatitis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsZhao, Z. / Wang, J.C. / Zlotnick, A.
Funding supportUnited States , 1件
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesR01-AI11893United States
CitationJournal: To Be Published
Title: Crystal structure of WHV core protein mutant Y132A dimer
Authors: Zhao, Z. / Wang, J. / Zlotnick, A.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Aug 9, 2018 / Release: May 1, 2019Array

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Assembly

Deposited unit
A: External core antigen
B: External core antigen
C: External core antigen
D: External core antigen


Theoretical massNumber of molelcules
Total (without water)68,5064
Polymers68,5064
Non-polymers00
Water0
1
A: External core antigen
B: External core antigen
C: External core antigen
D: External core antigen
x 60


Theoretical massNumber of molelcules
Total (without water)4,110,352240
Polymers4,110,352240
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: External core antigen
B: External core antigen
C: External core antigen
D: External core antigen
x 5


  • icosahedral pentamer
  • 343 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)342,52920
Polymers342,52920
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: External core antigen
B: External core antigen
C: External core antigen
D: External core antigen
x 6


  • icosahedral 23 hexamer
  • 411 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)411,03524
Polymers411,03524
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
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/peptide
External core antigen / capsid / HBeAg / Precore protein / p25


Mass: 17126.465 Da / Num. of mol.: 4 / Fragment: UNP residues 31-179
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Woodchuck hepatitis virus / Production host: Escherichia coli (E. coli) / References: UniProt: P0C6J4

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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: Woodchuck hepatitis virus / Type: VIRUS / Entity ID: 1 / Source: RECOMBINANT
Source (natural)Organism: Woodchuck hepatitis virus
Source (recombinant)Organism: Escherichia coli (E. coli)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 7.5
SpecimenConc.: 10 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: unspecified
VitrificationCryogen 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 FIELDBright-field microscopy
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameCategory
1EMAN2particle selection
2RELIONparticle selection
5EMAN2CTF correction
6RELIONCTF correction
9MDFFmodel fitting
10PHENIXmodel fitting
12PHENIXmodel refinement
15RELIONclassification
16RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7911 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 6ECS

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