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- EMDB-2059: Cryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid -

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Basic information

Entry
Database: EMDB / ID: 2059
TitleCryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid
Map dataCryo-EM structure of HBV T=4 pgRNA-filled Cp183 capsid (Cp183RNA-SSS)
SampleHBV T=4 pgRNA-filled Cp183 capsid:
virus
KeywordsHBV / Cp183 / pgRNA
SourceHepatitis B virus (HBV Cp183)
Methodsingle particle reconstruction / cryo EM / 8 Å resolution
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
DateDeposition: Mar 21, 2012 / Header (metadata) release: May 17, 2012 / Map release: Apr 3, 2013 / Last update: Jul 24, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 2
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_2059.map.gz (map file in CCP4 format, 106528 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
301 pix
1.48 Å/pix.
= 446.564 Å
301 pix
1.48 Å/pix.
= 446.564 Å
301 pix
1.48 Å/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
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum-4.96653509 - 9.94870949
Average (Standard dev.)0.13054132 (1.50642216)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions301301301
Origin-150-150-150
Limit150150150
Spacing301301301
CellA=B=C: 446.5636 Å
α=β=γ: 90.0 deg.

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-4.9679.9490.131

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Supplemental data

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Sample components

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Entire HBV T=4 pgRNA-filled Cp183 capsid

EntireName: HBV T=4 pgRNA-filled Cp183 capsid / Number of components: 1

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Component #1: virus, Hepatitis B virus

VirusName: Hepatitis B virus / a.k.a: HBV Cp183 / Class: VIRUS-LIKE PARTICLE
Details: Reassembled the purified Cp183 dimers with in vitro transcribed HBV pgRNA at a molar ratio of protein dimer to RNA polymer = 120:1
Empty: Yes / Enveloped: Yes / Isolate: STRAIN
SpeciesSpecies: Hepatitis B virus (HBV Cp183)
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: Cp183 / T number(triangulation number): 4

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 150 mM NaCl, 50 mM HEPES, 2 mM DTT / pH: 7.5
Support filmQuantifoil R 2/2 holey carbon 200 mesh copper grids
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 93 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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Electron microscopy imaging #1

ImagingMicroscope: JEOL 3200FS / Date: Apr 27, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 14 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
Cs: 1.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 270 - 3800 nm / Energy filter: Omega filter
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 97 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Electron microscopy imaging #2

ImagingMicroscope: JEOL 3200FS / Date: May 4, 2010
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 14 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 40000 X (nominal)
Astigmatism: objective lens astigmatism was corrected at 80,000 times magnification
Cs: 1.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 270 - 3800 nm / Energy filter: Omega filter
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 97 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 193

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 7201 / Applied symmetry: I (icosahedral)
3D reconstructionSoftware: Auto3dem / CTF correction: Each particle phase-flipping / Resolution: 8 Å / Resolution method: FSC 0.5

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