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- EMDB-2060: Cryo-EM structure of HBV T=4 empty Cp183 capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2060
TitleCryo-EM structure of HBV T=4 empty Cp183 capsid
Map dataCryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid at phosphorylation-mimic state (Cp183RNA-EEE)
Sample
  • Sample: HBV T=4 pgRNA-filled Cp183-EEE capsid
  • Virus: Hepatitis B virus
KeywordsHBV / Cp183 / Cp183-EEE / pgRNA
Biological speciesHepatitis B virus
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsWang JC-Y / Dhasan RS / Zlotnick A
CitationJournal: PLoS Pathog / Year: 2012
Title: Structural organization of pregenomic RNA and the carboxy-terminal domain of the capsid protein of hepatitis B virus.
Authors: Joseph C-Y Wang / Mary S Dhason / Adam Zlotnick /
Abstract: The Hepatitis B Virus (HBV) double-stranded DNA genome is reverse transcribed from its RNA pregenome (pgRNA) within the virus core (or capsid). Phosphorylation of the arginine-rich carboxy-terminal ...The Hepatitis B Virus (HBV) double-stranded DNA genome is reverse transcribed from its RNA pregenome (pgRNA) within the virus core (or capsid). Phosphorylation of the arginine-rich carboxy-terminal domain (CTD) of the HBV capsid protein (Cp183) is essential for pgRNA encapsidation and reverse transcription. However, the structure of the CTD remains poorly defined. Here we report sub-nanometer resolution cryo-EM structures of in vitro assembled empty and pgRNA-filled Cp183 capsids in unphosphorylated and phosphorylation-mimic states. In empty capsids, we found unexpected evidence of surface accessible CTD density partially occluding pores in the capsid surface. We also observed that CTD organization changed substantively as a function of phosphorylation. In RNA-filled capsids, unphosphorylated CTDs favored thick ropes of RNA, while the phosphorylation-mimic favored a mesh of thin, high-density strands suggestive of single stranded RNA. These results demonstrate that the CTD can regulate nucleic acid structure, supporting the hypothesis that the HBV capsid has a functional role as a nucleic acid chaperone.
History
DepositionMar 21, 2012-
Header (metadata) releaseMay 17, 2012-
Map releaseApr 3, 2013-
UpdateJul 24, 2013-
Current statusJul 24, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 35
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2060.jpg

Downloads & links

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Map

FileDownload / File: emd_2060.map.gz / Format: CCP4 / Size: 101.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid at phosphorylation-mimic state (Cp183RNA-EEE)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.48 Å/pix.
x 301 pix.
= 446.564 Å		1.48 Å/pix.
x 301 pix.
= 446.564 Å		1.48 Å/pix.
x 301 pix.
= 446.564 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4836 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 35.0 / Movie #1: 35
Minimum - Maximum-75.319999690000003 - 132.830001829999986
Average (Standard dev.)0.00535752 (±19.996448520000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions301301301
Spacing301301301
CellA=B=C: 446.5636 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.48360132890371.48360132890371.4836013289037
M x/y/z301301301
origin x/y/z0.0000.0000.000
length x/y/z446.564446.564446.564
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS301301301
D min/max/mean-75.320132.8300.005

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Supplemental data

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Sample components

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Entire : HBV T=4 pgRNA-filled Cp183-EEE capsid

EntireName: HBV T=4 pgRNA-filled Cp183-EEE capsid
Components
  • Sample: HBV T=4 pgRNA-filled Cp183-EEE capsid
  • Virus: Hepatitis B virus

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Supramolecule #1000: HBV T=4 pgRNA-filled Cp183-EEE capsid

SupramoleculeName: HBV T=4 pgRNA-filled Cp183-EEE 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-EEE
Details: Reassembled the purified Cp183-EEE dimers with in vitro transcribed HBV pgRNA at a molar ratio of protein dimer to RNA polymer = 120:1
NCBI-ID: 10407 / Sci species name: Hepatitis B virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: Yes / Syn species name: HBV Cp183-EEE
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: Cp183-EEE / 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

BufferpH: 7.4 / Details: 150mM NaCl, 50mM Tris, 2mM DTT
GridDetails: Quantifoil R 2/2 holey carbon 200 mesh copper grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 93 K / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

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Electron microscopy #1

Microscopy ID1
MicroscopeJEOL 3200FS
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
Specialist opticsEnergy filter - Name: Omega filter
DateMar 1, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 394 / 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: 4.87 µm / Nominal defocus min: 0.54 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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Electron microscopy #2

Microscopy ID2
MicroscopeJEOL 3200FS
TemperatureAverage: 97 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
Specialist opticsEnergy filter - Name: Omega filter
DateMay 18, 2011
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 394 / 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: 4.87 µm / Nominal defocus min: 0.54 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: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem / Number images used: 7439

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