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- EMDB-1403: Cryo-electron microscopy of hepatitis B virions reveals variabili... -

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Basic information

Entry
Database: EMDB / ID: EMD-1403
TitleCryo-electron microscopy of hepatitis B virions reveals variability in envelope capsid interactions.
Map data3d MAP OF SUB-SET OF HEPATITIS B VIRUS Particles (COMPACT PARTICLES; grouped in the same class)
Sample
  • Sample: Hepatitis B virus
  • Virus: Hepatitis B virus
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM
AuthorsSeitz S / Urban S / Antoni C / Bottcher B
CitationJournal: EMBO J / Year: 2007
Title: Cryo-electron microscopy of hepatitis B virions reveals variability in envelope capsid interactions.
Authors: Stefan Seitz / Stephan Urban / Christoph Antoni / Bettina Böttcher /
Abstract: Hepatitis B virus (HBV) is a major human pathogen causing about 750,000 deaths per year. The virion consists of a nucleocapsid and an envelope formed by lipids, and three integral membrane proteins. ...Hepatitis B virus (HBV) is a major human pathogen causing about 750,000 deaths per year. The virion consists of a nucleocapsid and an envelope formed by lipids, and three integral membrane proteins. Although we have detailed structural insights into the organization of the HBV core, the arrangement of the envelope in virions and its interaction with the nucleocapsid is elusive. Here we show the ultrastructure of hepatitis B virions purified from patient serum. We identified two morphological phenotypes, which appear as compact and gapped particles with nucleocapsids in distinguishable conformations. The overall structures of these nucleocapsids resemble recombinant cores with two alpha-helical spikes per asymmetric unit. At the charged tips the spikes are contacted by defined protrusions of the envelope proteins, probably via electrostatic interactions. The HBV envelope in the two morphotypes is to some extent variable, but the surface proteins follow a general packing scheme with up to three surface protein dimers per asymmetric unit. The variability in the structure of the envelope indicates that the nucleocapsid does not firmly constrain the arrangement of the surface proteins, but provides a general template for the packing.
History
DepositionAug 6, 2007-
Header (metadata) releaseAug 6, 2007-
Map releaseDec 6, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4.715180269
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 4.715180269
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1403.gif

Downloads & links

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Map

FileDownload / File: emd_1403.map.gz / Format: CCP4 / Size: 955.1 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation3d MAP OF SUB-SET OF HEPATITIS B VIRUS Particles (COMPACT PARTICLES; grouped in the same class)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
8.4 Å/pix.
x 63 pix.
= 529.2 Å		8.4 Å/pix.
x 63 pix.
= 529.2 Å		8.4 Å/pix.
x 63 pix.
= 529.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 8.4 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 13.1 / Movie #1: 4.7151803
Minimum - Maximum-54.157400000000003 - 63.7151
Average (Standard dev.)0.0100993 (±8.308070000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions636363
Spacing636363
CellA=B=C: 529.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z8.48.48.4
M x/y/z636363
origin x/y/z0.0000.0000.000
length x/y/z529.200529.200529.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-50-50-50
NX/NY/NZ100100100
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS636363
D min/max/mean-54.15763.7150.010

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Supplemental data

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Sample components

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Entire : Hepatitis B virus

EntireName: Hepatitis B virus
Components
  • Sample: Hepatitis B virus
  • Virus: Hepatitis B virus

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Supramolecule #1000: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: sample / ID: 1000 / Details: virus purified from patients serum / Number unique components: 1

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Name.synonym: HBV / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No / Syn species name: HBV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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

BufferpH: 7.4
GridDetails: 400 mesh copper rhodium grids (Maxtaform),
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: self made
Method: automatic blot for 1-2 seconds from both sides before plunging

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Electron microscopy

MicroscopeFEI/PHILIPS CM120T
TemperatureAverage: 178 K
Alignment procedureLegacy - Astigmatism: corrected at 200,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 21 µm / Number real images: 74 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Electron beamAcceleration voltage: 100 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 6.3 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.9 µm / Nominal magnification: 52000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailsparticles were selected manually
CTF correctionDetails: Each Particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Software - Name: MRC / Number images used: 16

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