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- EMDB-6687: Cryo-EM structure for Hepatitis A virus empty particle -

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Basic information

Entry
Database: EMDB / ID: 6687
TitleCryo-EM structure for Hepatitis A virus empty particle
Map dataCryo-EM map for HAV empty particle
SampleHepatitis A virusHepatitis A:
virus / VP1 / VP0 / VP3
Function / homologyHelicase/polymerase/peptidase polyprotein, Calicivirus-type / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / 3C cysteine protease (picornain 3C) ...Helicase/polymerase/peptidase polyprotein, Calicivirus-type / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / RNA-directed RNA polymerase, catalytic domain / Peptidase S1, PA clan / Viral coat protein subunit / Peptidase C3A/C3B, picornaviral / Helicase, superfamily 3, single-stranded DNA/RNA virus / Picornavirus/Calicivirus coat protein / 3C cysteine protease (picornain 3C) / Hepatitis A virus, protein VP1-2A / RNA dependent RNA polymerase / RNA helicase / Hepatitis A virus viral protein VP / RdRp of positive ssRNA viruses catalytic domain profile. / RNA-directed RNA polymerase, C-terminal domain / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Picornavirus capsid / 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 / 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 / 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
SourceHepatitis A virus
Methodsingle particle reconstruction / cryo EM / 3.9 Å resolution
AuthorsWang 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
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 ReportPDB-ID: 5wtf

SummaryFull reportAbout validation report
DateDeposition: Dec 11, 2016 / Header (metadata) release: Jan 25, 2017 / Map release: Jan 25, 2017 / Last update: Feb 8, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5wtf
  • Surface level: 0.05
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-5wtf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_6687.map.gz (map file in CCP4 format, 186625 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/pix.
= 486. Å
360 pix
1.35 Å/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 Level:0.018 (by author), 0.03 (movie #1):
Minimum - Maximum-0.10413745 - 0.16812561
Average (Standard dev.)0.0005952384 (0.0114673795)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions360360360
Origin-180.0-180.0-180.0
Limit179.0179.0179.0
Spacing360360360
CellA=B=C: 486.0 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-180-180-180
NC/NR/NS360360360
D min/max/mean-0.1040.1680.001

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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) / Vector: no plasmids / 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: 25.16134 kDa
SourceSpecies: Hepatitis A virus
Source (engineered)Expression System: Chlorocebus aethiops (grivet)
Source (natural)Organ or tissue: Homo sapiens

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Component #3: protein, VP0

ProteinName: VP0 / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 22.765881 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)

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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 (icosahedral) / Number of projections: 4000
3D reconstructionSoftware: Relion / Resolution: 3.9 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: 15
Output model

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