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- EMDB-6686: Cryo-EM structure for Hepatitis A virus full particle -

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Basic information

Entry
Database: EMDB / ID: EMD-6686
TitleCryo-EM structure for Hepatitis A virus full particle
Map data
SampleHepatitis A virus:
virus / VP1 / VP2 / VP3
Function / homology
Function and homology information


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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell ...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 / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / RNA-protein covalent cross-linking / integral to membrane of host cell / pore formation by virus in membrane of host cell / host multivesicular body / virion assembly / protein complex oligomerization / nucleoside-triphosphate phosphatase / ion channel activity / RNA-directed RNA polymerase / cysteine-type endopeptidase activity / viral RNA genome replication / RNA-directed 5'-3' RNA polymerase activity / RNA helicase activity / viral entry into host cell / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / integral component of membrane / ATP binding
Similarity search - Function
Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Superfamily 3 helicase of positive ssRNA viruses domain profile. ...Hepatitis A virus, protein VP1-2A / Hepatitis A virus viral protein VP / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded RNA virus / RNA helicase / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Reverse transcriptase/Diguanylate cyclase domain / Peptidase S1, PA clan, chymotrypsin-like fold / DNA/RNA polymerase superfamily / Peptidase S1, PA clan
Similarity search - Domain/homology
Biological speciesHepatitis A virus / Hepatovirus A
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsWang X / Zhu L / Dang M / Hu Z / Gao Q / Yuan S / Sun Y / Zhang B / Ren J / Walter TS ...Wang X / Zhu L / Dang M / Hu Z / Gao Q / Yuan S / Sun Y / Zhang B / Ren J / Walter TS / Wang J / Fry EE / Stuart DI / Rao Z
Funding support China, 1 items
OrganizationGrant numberCountry
National Science Foundation31570717 China
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 /
Abstract: Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and ...Hepatitis A virus (HAV) infects ∼1.4 million people annually and, although there is a vaccine, there are no licensed therapeutic drugs. HAV is unusually stable (making disinfection problematic) and little is known of how it enters cells and releases its RNA. Here we report a potent HAV-specific monoclonal antibody, R10, which neutralizes HAV infection by blocking attachment to the host cell. High-resolution cryo-EM structures of HAV full and empty particles and of the complex of HAV with R10 Fab reveal the atomic details of antibody binding and point to a receptor recognition site at the pentamer interface. These results, together with our observation that the R10 Fab destabilizes the capsid, suggest the use of a receptor mimic mechanism to neutralize virus infection, providing new opportunities for therapeutic intervention.
History
DepositionDec 11, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5wte
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5wte
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_6686.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 486. Å
1.35 Å/pix.
x 360 pix.
= 486. Å
1.35 Å/pix.
x 360 pix.
= 486. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.1587923 - 0.28721127
Average (Standard dev.)0.0025738906 (±0.016188819)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-180-180-180
Dimensions360360360
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z486.000486.000486.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.1590.2870.003

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Supplemental data

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Sample components

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Entire Hepatitis A virus

EntireName: Hepatitis A virus / Number of components: 4

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Component #1: virus, Hepatitis A virus

VirusName: Hepatitis A virusHepatitis A / Class: VIRION / Empty: No / Enveloped: No / Isolate: SEROTYPE
MassTheoretical: 6 MDa
SpeciesSpecies: Hepatitis A virus
Source (engineered)Expression System: Chlorocebus aethiops (grivet) / Cell of expression system: vero
Source (natural)Host Species: Homo sapiens (human)
Shell #1Name of element: capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Component #2: protein, VP1

ProteinName: VP1 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 30.820629 kDa
SourceSpecies: Hepatovirus A
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Component #3: protein, VP2

ProteinName: VP2 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 24.898172 kDa
SourceSpecies: Hepatitis A virus
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Component #4: protein, VP3

ProteinName: VP3 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 27.835693 kDa
SourceSpecies: Hepatitis A virus
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 2 mg/mL / Buffer solution: PBS Buffer / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 298 K / Humidity: 90 % / Details: blot for 3s seconds before plunging.

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Electron microscopy imaging

Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company
ImagingMicroscope: FEI POLARA 300
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 1.2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1200.0 - 3000.0 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 500

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (正20面体型対称) / Number of projections: 2500
3D reconstructionSoftware: RELION / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 120
Output model

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