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- EMDB-2278: cryoEM structure of hepatitis B virus core assembled from full-le... -

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Basic information

Entry
Database: EMDB / ID: EMD-2278
TitlecryoEM structure of hepatitis B virus core assembled from full-length core protein
Map dataReconstruction of HBV
Sample
  • Sample: Hepatitis B virus core assembled from full-length core protein
  • Virus: Hepatitis B virus
Keywordshepatitis B virus core antigen (HBc) / HBV capsid maturation and envelopment
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
Capsid protein / Capsid protein
Similarity search - Component
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsYu X / Jin L / Jih J / Shih C / Zhou ZH
CitationJournal: PLoS One / Year: 2013
Title: 3.5Å cryoEM structure of hepatitis B virus core assembled from full-length core protein.
Authors: Xuekui Yu / Lei Jin / Jonathan Jih / Chiaho Shih / Z Hong Zhou /
Abstract: The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was ...The capsid shell of infectious hepatitis B virus (HBV) is composed of 240 copies of a single protein called HBV core antigen (HBc). An atomic model of a core assembled from truncated HBc was determined previously by X-ray crystallography. In an attempt to obtain atomic structural information of HBV core in a near native, non-crystalline environment, we reconstructed a 3.5Å-resolution structure of a recombinant core assembled from full-length HBc by cryo electron microscopy (cryoEM) and derived an atomic model. The structure shows that the 240 molecules of full-length HBc form a core with two layers. The outer layer, composed of the N-terminal assembly domain, is similar to the crystal structure of the truncated HBc, but has three differences. First, unlike the crystal structure, our cryoEM structure shows no disulfide bond between the Cys61 residues of the two subunits within the dimer building block, indicating such bond is not required for core formation. Second, our cryoEM structure reveals up to four more residues in the linker region (amino acids 140-149). Third, the loops in the cryoEM structures containing this linker region in subunits B and C are oriented differently (~30° and ~90°) from their counterparts in the crystal structure. The inner layer, composed of the C-terminal arginine-rich domain (ARD) and the ARD-bound RNAs, is partially-ordered and connected with the outer layer through linkers positioned around the two-fold axes. Weak densities emanate from the rims of positively charged channels through the icosahedral three-fold and local three-fold axes. We attribute these densities to the exposed portions of some ARDs, thus explaining ARD's accessibility by proteases and antibodies. Our data supports a role of ARD in mediating communication between inside and outside of the core during HBV maturation and envelopment.
History
DepositionJan 11, 2013-
Header (metadata) releaseJan 30, 2013-
Map releaseOct 2, 2013-
UpdateOct 2, 2013-
Current statusOct 2, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j2v
  • Surface level: 3.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j2v
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2278-HBV...

Downloads & links

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Map

FileDownload / File: emd_2278.map.gz / Format: CCP4 / Size: 317.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of HBV
Voxel sizeX=Y=Z: 0.9333 Å
Density
Contour LevelBy EMDB: 1.35 / Movie #1: 3.5
Minimum - Maximum-9.45280552 - 15.384388919999999
Average (Standard dev.)0.04746093 (±1.25213301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-220-220-220
Dimensions440440440
Spacing440440440
CellA=B=C: 410.652 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.93330.93330.9333
M x/y/z440440440
origin x/y/z0.0000.0000.000
length x/y/z410.652410.652410.652
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-30-80
NX/NY/NZ7361161
MAP C/R/S123
start NC/NR/NS-220-220-220
NC/NR/NS440440440
D min/max/mean-9.45315.3840.047

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Supplemental data

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Sample components

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Entire : Hepatitis B virus core assembled from full-length core protein

EntireName: Hepatitis B virus core assembled from full-length core protein
Components
  • Sample: Hepatitis B virus core assembled from full-length core protein
  • Virus: Hepatitis B virus

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Supramolecule #1000: Hepatitis B virus core assembled from full-length core protein

SupramoleculeName: Hepatitis B virus core assembled from full-length core protein
type: sample / ID: 1000 / Oligomeric state: Icosahedral particle / Number unique components: 1
Molecular weightExperimental: 5 MDa / Theoretical: 5 MDa / Method: Based on amino acid sequences

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Escherichia coli (E. coli) / Recombinant plasmid: pET-11a
Molecular weightExperimental: 5 MDa / Theoretical: 5 MDa
Virus shellShell ID: 1 / Diameter: 360 Å / T number (triangulation number): 4

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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

VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK II

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.75 mm / Nominal magnification: 75000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
DateJan 1, 2009
Image recordingDigitization - Scanner: NIKON SUPER COOLSCAN 9000 / Average electron dose: 25 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: IMIRS / Number images used: 8093

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