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- PDB-5wte: Cryo-EM structure for Hepatitis A virus full particle -

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Basic information

Entry
Database: PDB / ID: 5wte
TitleCryo-EM structure for Hepatitis A virus full particle
Components
  • VP1
  • VP2
  • VP3
KeywordsVIRUS / HAV / Neutralizing mechanism / Receptor recognition / Viral entry
Function / homologyHelicase/polymerase/peptidase polyprotein, Calicivirus-type / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Hepatitis A virus, protein VP1-2A / RNA-directed RNA polymerase, catalytic domain / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / 3C cysteine protease (picornain 3C) ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Hepatitis A virus, protein VP1-2A / RNA-directed RNA polymerase, catalytic domain / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Helicase, superfamily 3, single-stranded DNA/RNA virus / 3C cysteine protease (picornain 3C) / RNA-directed RNA polymerase, C-terminal domain / Picornavirus capsid / Superfamily 3 helicase of positive ssRNA viruses domain profile. / RNA dependent RNA polymerase / Peptidase S1, PA clan / RdRp of positive ssRNA viruses catalytic domain profile. / Hepatitis A virus viral protein VP / RNA helicase / host cell mitochondrial outer membrane / negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / suppression by virus of host MAVS activity / picornain 3C / RNA-protein covalent cross-linking / host cell cytoplasmic vesicle membrane / pore formation by virus in membrane of host cell / integral to membrane of host cell / RNA helicase activity / nucleoside-triphosphate phosphatase / virion assembly / host multivesicular body / viral capsid / RNA-directed RNA polymerase / ion channel activity / protein complex oligomerization / viral RNA genome replication / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / cysteine-type endopeptidase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / integral component of membrane / ATP binding / Genome polyprotein
Function and homology information
Specimen sourceHepatovirus A
Hepatitis A virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 3.4 Å resolution
AuthorsWang, X. / Zhu, L. / Dang, M. / Hu, Z. / Gao, Q. / Yuan, S. / Sun, Y. / Zhang, B. / Ren, J. / Walter, T.S. / Wang, J. / Fry, E.E. / Stuart, D.I. / Rao, Z.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Potent neutralization of hepatitis A virus reveals a receptor mimic mechanism and the receptor recognition site.
Authors: Xiangxi Wang / Ling Zhu / Minghao Dang / Zhongyu Hu / Qiang Gao / Shuai Yuan / Yao Sun / Bo Zhang / Jingshan Ren / Abhay Kotecha / Thomas S Walter / Junzhi Wang / Elizabeth E Fry / David I Stuart / Zihe Rao
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 11, 2016 / Release: Jan 25, 2017
RevisionDateData content typeGroupProviderType
1.0Jan 25, 2017Structure modelrepositoryInitial release
1.1Feb 1, 2017Structure modelOther / Structure summary
1.2Feb 8, 2017Structure modelDatabase references

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Structure visualization

Movie
  • 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
  • EMDB-6686
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  • Superimposition on EM map
  • EMDB-6686
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP2
C: VP3


Theoretical massNumber of molelcules
Total (without water)83,5543
Polyers83,5543
Non-polymers00
Water0
1
A: VP1
B: VP2
C: VP3
x 60


Theoretical massNumber of molelcules
Total (without water)5,013,270180
Polyers5,013,270180
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: VP1
B: VP2
C: VP3
x 5


  • icosahedral pentamer
  • 418 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)417,77215
Polyers417,77215
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: VP1
B: VP2
C: VP3
x 6


  • icosahedral 23 hexamer
  • 501 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)501,32718
Polyers501,32718
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
6
A: VP1
B: VP2
C: VP3
x 60


  • crystal asymmetric unit, crystal frame
  • 5.01 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)5,013,270180
Polyers5,013,270180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60

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Components

#1: Protein/peptide VP1


Mass: 30820.629 Da / Num. of mol.: 1 / Fragment: UNP residues 20-289 / Mutation: K37R, S178Q / Source: (gene. exp.) Hepatovirus A / Organ: Homo sapiens / Cell line (production host): Vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*PLUS
#2: Protein/peptide VP2


Mass: 24898.172 Da / Num. of mol.: 1 / Source: (gene. exp.) Hepatitis A virus / Organ: Homo sapiens / Cell line (production host): vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*PLUS
#3: Protein/peptide VP3


Mass: 27835.693 Da / Num. of mol.: 1 / Source: (gene. exp.) Hepatitis A virus / Organ: Homo sapiens / Cell line (production host): vero / Production host: Chlorocebus aethiops (grivet) / References: UniProt: P08617*PLUS

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Hepatitis A virusHepatitis A / Type: VIRUS / Entity ID: 1, 2, 3 / Source: RECOMBINANT
Molecular weightValue: 6 MDa / Experimental value: NO
Source (natural)Organism: Hepatitis A virus
Source (recombinant)Cell: vero / Organism: Chlorocebus aethiops (grivet)
Details of virusEmpty: NO / Virus isolate: SEROTYPE / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Virus shellName: capsid / Diameter: 300 nm / Triangulation number (T number): 1
Buffer solutionDetails: PBS Buffer / pH: 7.4
SpecimenConc.: 2 mg/ml / Details: This sample was monodisperse / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 400 / Grid type: C-Flat
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 kelvins / Details: blot for 3s seconds before plunging

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
MicroscopyMicroscope model: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3000 nm / Nominal defocus min: 1200 nm / Calibrated defocus min: 1200 nm / Calibrated defocus max: 3000 nm / Cs: 2 mm
Specimen holderSpecimen holder model: OTHER
Image recordingAverage exposure time: 1.8 sec. / Electron dose: 1.2 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number of grids imaged: 4 / Number of real images: 500
Image scansWidth: 3710 / Height: 3710 / Movie frames/image: 25 / Used frames/image: 1-25

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Processing

SoftwareName: PHENIX / Version: 1.10.1_2155: / Classification: refinement
EM software
IDNameVersionCategoryDetails
1EMAN2.0particle selectionEMAN2 e2boxer.py was used to automatically select particle images
4Gctf3.0CTF correction
7CHIMERAmodel fitting
10Relion1.3final Euler assignment
12Relion1.33D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNumber of particles selected: 3000
SymmetryPoint symmetry: I
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number of particles: 2500 / Number of class averages: 35 / Symmetry type: POINT
Atomic model buildingOverall b value: 120 / Ref protocol: AB INITIO MODEL / Ref space: REAL / Target criteria: Correlation coefficient

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