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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: EMD-6687
TitleCryo-EM structure for Hepatitis A virus empty particle
Map dataCryo-EM map for HAV empty particle
Sample
  • Virus: Hepatitis A virus
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3
KeywordsHAV / Neutralizing mechanism / Receptor recognition / Viral entry / VIRUS
Function / homology
Function and homology information


host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport ...host cell mitochondrial outer membrane / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / picornain 3C / ribonucleoside triphosphate phosphatase activity / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / host multivesicular body / nucleoside-triphosphate phosphatase / channel activity / monoatomic ion transmembrane transport / RNA helicase activity / symbiont entry into host cell / RNA-directed RNA polymerase / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / DNA-templated transcription / virion attachment to host cell / structural molecule activity / proteolysis / RNA binding / ATP binding / membrane
Similarity search - Function
Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid ...Hepatitis A virus, protein VP1-2A / : / Hepatitis A virus viral protein VP / 2B protein soluble domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily
Similarity search - Domain/homology
Biological speciesHepatitis A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWang X / Zhu L
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-
UpdateMar 27, 2024-
Current statusMar 27, 2024Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.03
  • Imaged by UCSF Chimera
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  • 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 modelsPDB-5wtf
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6687.png

Downloads & links

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Map

FileDownload / File: emd_6687.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map for HAV empty particle
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

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.03
Minimum - Maximum-0.10413745 - 0.16812561
Average (Standard dev.)0.0005952384 (±0.0114673795)
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-0.1040.1680.001

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Supplemental data

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Sample components

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Entire : Hepatitis A virus

EntireName: Hepatitis A virus
Components
  • Virus: Hepatitis A virus
    • Protein or peptide: VP1
    • Protein or peptide: VP0
    • Protein or peptide: VP3

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Supramolecule #1: Hepatitis A virus

SupramoleculeName: Hepatitis A virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 12092 / Sci species name: Hepatitis A virus / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 6 MDa
Virus shellShell ID: 1 / Name: capsid / Diameter: 300.0 Å / T number (triangulation number): 1

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Macromolecule #1: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis A virus / Organ: Homo sapiens
Molecular weightTheoretical: 25.16134 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: VGAITTIEDP VLAKKVPETF PELKPGESRH TSDHMSIYKF MGRSHFLCTF TFNSNNKEYT FPITLSSTSN PPHGLPSTLR WFFNLFQLY RGPLDLTIII TGATDVDGMA WFTPVGLAVD TPWVEKESAL QIDYKTALGA VRFNTRRTGN IQIRLPWYSY L YAVSGALD ...String:
VGAITTIEDP VLAKKVPETF PELKPGESRH TSDHMSIYKF MGRSHFLCTF TFNSNNKEYT FPITLSSTSN PPHGLPSTLR WFFNLFQLY RGPLDLTIII TGATDVDGMA WFTPVGLAVD TPWVEKESAL QIDYKTALGA VRFNTRRTGN IQIRLPWYSY L YAVSGALD GLGDKTDSTF GLVSIQIANY NHSDEYLSFS CYLSVTEQSE FYFPRAPLNS NAMLST

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Macromolecule #2: VP0

MacromoleculeName: VP0 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis A virus / Organ: Homo sapiens
Molecular weightTheoretical: 22.765881 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: ASYFTSVDQS SVHTAEVGSH QIEPLKTSVD KPGSKKTQGE KFFLIHSARW LTTHALFHEV AKLDVVKLLY NEQFAVQGLL RYHTYARFG IEIQVQINPT PFQQGGLICA MVPGDQSYGS IASLTVYPHG LLNCNINNVV RIKVPFIYTR GAYHFKDPQY P VWELTIRV ...String:
ASYFTSVDQS SVHTAEVGSH QIEPLKTSVD KPGSKKTQGE KFFLIHSARW LTTHALFHEV AKLDVVKLLY NEQFAVQGLL RYHTYARFG IEIQVQINPT PFQQGGLICA MVPGDQSYGS IASLTVYPHG LLNCNINNVV RIKVPFIYTR GAYHFKDPQY P VWELTIRV WSELNIGTGT SAYTSLNVLA RFTDLELHGL TPLST

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Macromolecule #3: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Hepatitis A virus
Molecular weightTheoretical: 27.835693 KDa
Recombinant expressionOrganism: Chlorocebus aethiops (grivet)
SequenceString: MMRNETRVST TENVVNLSNY EDARAKMSFA LDQEDWKSDP SQGGGIKITH FTTWTSIPTL AAQFPFNASD SVGQQIKVIP VDPYFFQMT NTNPDQKCIT ALASICQMFC FWRGDLVFDF QVFPTKYHSG RLLFCFVPGN ELIDVTGITL KQATTAPCAV M DIAGVQST ...String:
MMRNETRVST TENVVNLSNY EDARAKMSFA LDQEDWKSDP SQGGGIKITH FTTWTSIPTL AAQFPFNASD SVGQQIKVIP VDPYFFQMT NTNPDQKCIT ALASICQMFC FWRGDLVFDF QVFPTKYHSG RLLFCFVPGN ELIDVTGITL KQATTAPCAV M DIAGVQST LRFRVPWISD TPYRVNRYTK EAHQKGEYTA IGKLIVYCYN RLTSPSNVAH HVRVNVYLSA INLECFAPLY HA MDVTTQ

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration2 mg/mL
BufferpH: 7.4 / Details: PBS Buffer
GridModel: C-flat / Material: COPPER / Mesh: 400 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 60 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK III / Details: blot for 3s seconds before plunging.
DetailsThis sample was monodisperse

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3710 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-25 / Number grids imaged: 4 / Number real images: 500 / Average exposure time: 1.8 sec. / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus max: 3.0 µm / Calibrated defocus min: 1.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.2 µm
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 5000
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4qpg

Final reconstructionNumber classes used: 45 / Applied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.3) / Number images used: 4000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING
Projection matching processing - Merit function: Correlation coefficient
Projection matching processing - Angular sampling: 0.375 degrees
Software - Name: RELION (ver. 1.3)
Final 3D classificationNumber classes: 50 / Avg.num./class: 60

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 150 / Target criteria: Correlation coefficient
Output model

PDB-5wtf:
Cryo-EM structure for Hepatitis A virus empty particle

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