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- EMDB-1158: Hepatitis B small surface antigen particles are octahedral. -

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Basic information

Entry
Database: EMDB / ID: EMD-1158
TitleHepatitis B small surface antigen particles are octahedral.
Map dataElectron density map of an octahedral small Hepatitis B surface antigen particle
Sample
  • Sample: Hepatitis B small surface antigen
  • Protein or peptide: surface antigen
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
AuthorsGilbert RJC / Beales L / Blond D / Simon MN / Lin BY / Chisari FV / Stuart DI / Rowlands DJ
CitationJournal: Proc Natl Acad Sci U S A / Year: 2005
Title: Hepatitis B small surface antigen particles are octahedral.
Authors: Robert J C Gilbert / Lucy Beales / Donatienne Blond / Martha N Simon / Beth Y Lin / Francis V Chisari / David I Stuart / David J Rowlands /
Abstract: The infectious component of hepatitis B (HB) virus (HBV), the Dane particle, has a diameter of approximately 44 nm and consists of a double-layered capsid particle enclosing a circular, incomplete ...The infectious component of hepatitis B (HB) virus (HBV), the Dane particle, has a diameter of approximately 44 nm and consists of a double-layered capsid particle enclosing a circular, incomplete double-stranded DNA genome. The outer capsid layer is formed from the HB surface antigen (HBsAg) and lipid, whereas the inner layer is formed from the HB core Ag assembled into an icosahedral structure. During chronic infection HBsAg is expressed in large excess as noninfectious quasispherical particles and tubules with approximately 22-nm diameter. Here, we report cryo-EM reconstructions of spherical HBsAg particles at approximately 12-A resolution. We show that the particles possess different diameters and have separated them into two predominant populations, both of which have octahedral symmetry. Despite their differing diameters, the two forms of the particle have the same mass and are built through conformational switching of the same building block, a dimer of HBsAg. We propose that this conformational switching, combined with interactions with the underlying core, leads to the formation of HBV Dane particles of different sizes, dictated by the symmetry of the icosahedral core.
History
DepositionSep 10, 2005-
Header (metadata) releaseSep 10, 2005-
Map releaseSep 10, 2006-
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: 170
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 170
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1158.gif

Downloads & links

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Map

FileDownload / File: emd_1158.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationElectron density map of an octahedral small Hepatitis B surface antigen particle
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
2.74 Å/pix.
x 128 pix.
= 350.4 Å		2.74 Å/pix.
x 128 pix.
= 350.4 Å		2.74 Å/pix.
x 128 pix.
= 350.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7375 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 85.900000000000006 / Movie #1: 170
Minimum - Maximum-473.117000000000019 - 959.522000000000048
Average (Standard dev.)-0.00000000910157 (±71.668000000000006)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 350.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.73752.73752.7375
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z350.400350.400350.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S312
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-473.117959.522-0.000

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Supplemental data

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Sample components

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Entire : Hepatitis B small surface antigen

EntireName: Hepatitis B small surface antigen
Components
  • Sample: Hepatitis B small surface antigen
  • Protein or peptide: surface antigen

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Supramolecule #1000: Hepatitis B small surface antigen

SupramoleculeName: Hepatitis B small surface antigen / type: sample / ID: 1000
Details: The sample was a mixed population of smaller and larger particles; this is a map of the smaller kind
Oligomeric state: An octahedral structure consisting of 48 / Number unique components: 1
Molecular weightExperimental: 2.18 MDa / Theoretical: 2.04 MDa
Method: Volumetrically, also by STEM and fitting of atomic models

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Macromolecule #1: surface antigen

MacromoleculeName: surface antigen / type: protein_or_peptide / ID: 1 / Name.synonym: sAg / Details: 48 sAg proteins compose the particle reconstructed / Number of copies: 48 / Oligomeric state: 48 copies obeying octahedral symmetry / Recombinant expression: Yes
Source (natural)Organism: Hepatitis B virus / Tissue: Mouse serum
Molecular weightExperimental: 24 KDa / Theoretical: 24 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)

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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

Concentration0.3 mg/mL
BufferpH: 7.2 / Details: PBS
GridDetails: 300 mesh copper grid bearing holey carbon film
VitrificationCryogen name: ETHANE / Chamber temperature: 20 K / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Simple guillotone / Method: Blot until grid draws away from paper

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureAverage: 100 K
Alignment procedureLegacy - Astigmatism: Astigmatism corrected at 135,000 magnification
DateJun 1, 2000
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 8.33 µm / Number real images: 17 / Average electron dose: 2 e/Å2 / Od range: 5 / Bits/pixel: 8
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 7.21 µm / Nominal defocus min: 1.79 µm / Nominal magnification: 38000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using Ximdisp
CTF correctionDetails: by micrograph
Final reconstructionApplied symmetry - Point group: O (octahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: OTHER / Software - Name: IMAGIC, FREALIGN and SPIDER
Details: Single particles were reconstructed in IMAGIC using D2 symmetry and then in FREALIGN using tetrahedral symmetry. Maps were shown to in fact have octahedral symmetry. Reconstruction was ...Details: Single particles were reconstructed in IMAGIC using D2 symmetry and then in FREALIGN using tetrahedral symmetry. Maps were shown to in fact have octahedral symmetry. Reconstruction was iterative and has symmetry determination and size fractionation coupled.
Number images used: 911
Final angle assignmentDetails: SPIDER

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