[English] 日本語
Yorodumi
- EMDB-6687: Cryo-EM structure for Hepatitis A virus empty particle -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-6687
TitleCryo-EM structure for Hepatitis A virus empty particle
Map data
SampleHepatitis A virus:
virus / VP1 / VP0 / VP3
Function / homology
Function and homology information


host cell mitochondrial outer membrane / negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / picornain 3C / suppression by virus of host MAVS activity / 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 ...host cell mitochondrial outer membrane / negative regulation of toll-like receptor 3 signaling pathway / icosahedral viral capsid / picornain 3C / suppression by virus of host MAVS activity / 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 / nucleoside-triphosphate phosphatase / virion assembly / protein complex oligomerization / host multivesicular body / RNA-directed RNA polymerase / ion channel activity / viral RNA genome replication / RNA helicase activity / cysteine-type endopeptidase activity / viral entry into host cell / RNA-directed 5'-3' RNA polymerase activity / transcription, DNA-templated / virion attachment to host cell / structural molecule activity / RNA binding / integral component of membrane / ATP binding
Peptidase C3A/C3B, picornaviral / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Hepatitis A virus, protein VP1-2A / Helicase, superfamily 3, single-stranded RNA virus / Peptidase S1, PA clan / RNA-directed RNA polymerase, C-terminal domain / RNA-directed RNA polymerase, catalytic domain / Helicase/polymerase/peptidase polyprotein, Calicivirus-type / Picornavirus capsid / Helicase, superfamily 3, single-stranded DNA/RNA virus
Genome polyprotein
Biological speciesHepatitis A virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
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
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.
Validation ReportPDB-ID: 5wtf

SummaryFull reportAbout validation report
History
DepositionDec 11, 2016-
Header (metadata) releaseJan 25, 2017-
Map releaseJan 25, 2017-
UpdateNov 6, 2019-
Current statusNov 6, 2019Processing site: PDBj / Status: Released

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

Downloads & links

-
Map

FileDownload / File: emd_6687.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: 0.03
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

-
Supplemental data

-
Sample components

-
Entire Hepatitis A virus

EntireName: Hepatitis A virus / Number of components: 4

-
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

-
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

-
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

-
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)

-
Experimental details

-
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.

-
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)

-
Image acquisition

Image acquisitionNumber of digital images: 500

-
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

-
Atomic model buiding

Modeling #1Target criteria: Correlation coefficient / Refinement space: REAL / Overall bvalue: 150
Output model

+
About Yorodumi

-
News

-
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

-
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force. (see PDBe EMDB page)
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is "EMD"? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB at PDBe / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.:Changes in new EM Navigator and Yorodumi

Read more

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more