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- EMDB-1969: The cryo-EM structure of HBV Cp183 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-1969
TitleThe cryo-EM structure of HBV Cp183 capsid
Map dataThis is a cryo-EM 3D map of HBV Cp183 capsid
Sample
  • Sample: HBV Cp183 capsid
  • Virus: Hepatitis B virus
KeywordsHBV / Cp183
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 17.4 Å
AuthorsChen C / Wang JC-Y / Zlotnick A
CitationJournal: PLoS Pathog / Year: 2011
Title: A kinase chaperones hepatitis B virus capsid assembly and captures capsid dynamics in vitro.
Authors: Chao Chen / Joseph Che-Yen Wang / Adam Zlotnick /
Abstract: The C-terminal domain (CTD) of Hepatitis B virus (HBV) core protein is involved in regulating multiple stages of the HBV lifecycle. CTD phosphorylation correlates with pregenomic-RNA encapsidation ...The C-terminal domain (CTD) of Hepatitis B virus (HBV) core protein is involved in regulating multiple stages of the HBV lifecycle. CTD phosphorylation correlates with pregenomic-RNA encapsidation during capsid assembly, reverse transcription, and viral transport, although the mechanisms remain unknown. In vitro, purified HBV core protein (Cp183) binds any RNA and assembles aggressively, independent of phosphorylation, to form empty and RNA-filled capsids. We hypothesize that there must be a chaperone that binds the CTD to prevent self-assembly and nonspecific RNA packaging. Here, we show that HBV capsid assembly is stalled by the Serine Arginine protein kinase (SRPK) binding to the CTD, and reactivated by subsequent phosphorylation. Using the SRPK to probe capsids, solution and structural studies showed that SRPK bound to capsid, though the CTD is sequestered on the capsid interior. This result indicates transient CTD externalization and suggests that capsid dynamics could be crucial for directing HBV intracellular trafficking. Our studies illustrate the stochastic nature of virus capsids and demonstrate the appropriation of a host protein by a virus for a non-canonical function.
History
DepositionSep 20, 2011-
Header (metadata) releaseSep 5, 2012-
Map releaseSep 5, 2012-
UpdateSep 5, 2012-
Current statusSep 5, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 20
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 20
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-1969.png

Downloads & links

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Map

FileDownload / File: emd_1969.map.gz / Format: CCP4 / Size: 30.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a cryo-EM 3D map of HBV Cp183 capsid
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.94 Å/pix.
x 201 pix.
= 590.94 Å		2.94 Å/pix.
x 201 pix.
= 590.94 Å		2.94 Å/pix.
x 201 pix.
= 590.94 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 20.0 / Movie #1: 20
Minimum - Maximum-104.059997559999999 - 198.539993290000012
Average (Standard dev.)0.00489897 (±19.998184200000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions201201201
Spacing201201201
CellA=B=C: 590.94 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.942.942.94
M x/y/z201201201
origin x/y/z0.0000.0000.000
length x/y/z590.940590.940590.940
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-100-100-100
NC/NR/NS201201201
D min/max/mean-104.060198.5400.005

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Supplemental data

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Sample components

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Entire : HBV Cp183 capsid

EntireName: HBV Cp183 capsid
Components
  • Sample: HBV Cp183 capsid
  • Virus: Hepatitis B virus

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Supramolecule #1000: HBV Cp183 capsid

SupramoleculeName: HBV Cp183 capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Hepatitis B virus

SupramoleculeName: Hepatitis B virus / type: virus / ID: 1 / Name.synonym: HBV Cp183 / Details: HBV Cp183 was purified from E. coli / NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes / Syn species name: HBV Cp183
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: Cp183 / 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

Concentration0.24 mg/mL
BufferpH: 7.4 / Details: 0.53 M NaCl, 10 mM DTT, 20 mM Tris-HCl
GridDetails: Quantifoil R 2/2 holey carbon 200 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FS
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
Specialist opticsEnergy filter - Name: Omega filter
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 19 / Average electron dose: 14 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 1.1 mm / Nominal defocus max: 2.09 µm / Nominal defocus min: 1.23 µm / Nominal magnification: 80000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle phase-flipping
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 17.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 955

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