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- EMDB-5173: Cryo-EM structure of virion-sized hepatitis E virus-like particle -

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Basic information

Entry
Database: EMDB / ID: EMD-5173
TitleCryo-EM structure of virion-sized hepatitis E virus-like particle
Map dataThis is a map for the virion-sized hepatitis E virus-like particle
Sample
  • Sample: Hepatitis E virus like particle
  • Virus: Hepatitis E virus
Keywordsassembly pathway
Function / homology
Function and homology information


host cell endoplasmic reticulum / T=1 icosahedral viral capsid / host cell surface / host cell Golgi apparatus / structural molecule activity / RNA binding / extracellular region / identical protein binding
Similarity search - Function
Hepatitis E virus structural protein 2 / Structural protein 2 nucleoplasmin-like domain / : / Structural protein 2 second domain / : / Structural protein 2 C-terminal domain / Viral coat protein subunit
Similarity search - Domain/homology
Pro-secreted protein ORF2
Similarity search - Component
Biological speciesHepatitis E virus
Methodsingle particle reconstruction / cryo EM / Resolution: 10.5 Å
AuthorsXing L / Mayazaki N / Li TC / Simons MN / Wall JS / Moore M / Wang CY / Takeda N / Wakita T / Miyamura T / Cheng RH
CitationJournal: J Biol Chem / Year: 2010
Title: Structure of hepatitis E virion-sized particle reveals an RNA-dependent viral assembly pathway.
Authors: Li Xing / Tian-Cheng Li / Naoyuki Mayazaki / Martha N Simon / Joseph S Wall / Mary Moore / Che-Yen Wang / Naokazu Takeda / Takaji Wakita / Tatsuo Miyamura / R Holland Cheng /
Abstract: Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. ...Hepatitis E virus (HEV) induces acute hepatitis in humans with a high fatality rate in pregnant women. There is a need for anti-HEV research to understand the assembly process of HEV native capsid. Here, we produced a large virion-sized and a small T=1 capsid by expressing the HEV capsid protein in insect cells with and without the N-terminal 111 residues, respectively, for comparative structural analysis. The virion-sized capsid demonstrates a T=3 icosahedral lattice and contains RNA fragment in contrast to the RNA-free T=1 capsid. However, both capsids shared common decameric organization. The in vitro assembly further demonstrated that HEV capsid protein had the intrinsic ability to form decameric intermediate. Our data suggest that RNA binding is the extrinsic factor essential for the assembly of HEV native capsids.
History
DepositionMar 9, 2010-
Header (metadata) releaseAug 9, 2010-
Map releaseAug 9, 2010-
UpdateOct 11, 2011-
Current statusOct 11, 2011Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 6.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3iyo
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3iyo
  • Surface level: 6.5
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iyo
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5173_1.png

Downloads & links

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Map

FileDownload / File: emd_5173.map.gz / Format: CCP4 / Size: 118.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map for the virion-sized hepatitis E virus-like particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2 Å/pix.
x 317 pix.
= 634. Å		2 Å/pix.
x 317 pix.
= 634. Å		2 Å/pix.
x 317 pix.
= 634. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 5.2 / Movie #1: 6.5
Minimum - Maximum-22.952999999999999 - 30.429300000000001
Average (Standard dev.)-0.0644812 (±3.54616)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-159-159-159
Dimensions317317317
Spacing317317317
CellA=B=C: 634 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z317317317
origin x/y/z0.0000.0000.000
length x/y/z634.000634.000634.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-159-159-159
NC/NR/NS317317317
D min/max/mean-22.95330.429-0.064

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Supplemental data

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Sample components

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Entire : Hepatitis E virus like particle

EntireName: Hepatitis E virus like particle
Components
  • Sample: Hepatitis E virus like particle
  • Virus: Hepatitis E virus

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Supramolecule #1000: Hepatitis E virus like particle

SupramoleculeName: Hepatitis E virus like particle / type: sample / ID: 1000 / Oligomeric state: 1 / Number unique components: 2
Molecular weightExperimental: 11.8 MDa / Theoretical: 12.2 MDa / Method: STEM

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Supramolecule #1: Hepatitis E virus

SupramoleculeName: Hepatitis E virus / type: virus / ID: 1 / Name.synonym: recombinant virus-like particle / NCBI-ID: 12461 / Sci species name: Hepatitis E virus / Database: NCBI / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SEROTYPE / Virus enveloped: No / Virus empty: No / Syn species name: recombinant virus-like particle
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightExperimental: 11.8 MDa / Theoretical: 12.2 MDa
Virus shellShell ID: 1 / Name: ORF2 protein / Diameter: 410 Å / T number (triangulation number): 3

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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

Concentration1 mg/mL
BufferpH: 6.2 / Details: 20mM MES-K
GridDetails: 300 mesh holey carbon
VitrificationCryogen name: ETHANE / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: manual plunger

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Electron microscopy

MicroscopeJEOL 2100F
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F415 (4k x 4k) / Average electron dose: 10 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal magnification: 50000
Sample stageSpecimen holder: single-tilt / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: each micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: P3DR / Number images used: 4348

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Atomic model buiding 1

Initial modelPDB ID:

2zzq


Chain - Chain ID: A
SoftwareName: Situs
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. Monomer C were divided into Shell and Spike domains and separately fitted by manual docking using program O and followed by Situs
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross-correlation
Output model

PDB-3iyo:
Cryo-EM model of virion-sized HEV virion-sized capsid

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