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- EMDB-3269: Importin-beta can bind Hepatitis B Virus core protein and empty c... -

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Basic information

Entry
Database: EMDB / ID: 3269
TitleImportin-beta can bind Hepatitis B Virus core protein and empty core-like particles and induce structural changes
Map dataCryo-EM reconstruction of unphosphorylated Cp183 and Imp-beta in ammonium formate
Sample11 uM Cp183 dimer in capsid form and 18.8 uM Imp-beta in ammonium formate:
virus / importin betaImportin
KeywordsHBV / Cp183 / Importin-beta
SourceHepatitis B virus (HBV) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / 10.1 Å resolution
AuthorsChen C / Wang JC-Y / Pierson EE / Kiefer DZ / Delaleau M / Gallucci L / Cazenave C / Kann M / Jarrold MF / Zlotnick A
CitationJournal: PLoS Pathog. / Year: 2016
Title: Importin β Can Bind Hepatitis B Virus Core Protein and Empty Core-Like Particles and Induce Structural Changes.
Authors: Chao Chen / Joseph Che-Yen Wang / Elizabeth E Pierson / David Z Keifer / Mildred Delaleau / Lara Gallucci / Christian Cazenave / Michael Kann / Martin F Jarrold / Adam Zlotnick
DateDeposition: Dec 1, 2015 / Header (metadata) release: Jan 27, 2016 / Map release: Aug 24, 2016 / Last update: Aug 24, 2016

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.25
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.25
  • 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_3269.map.gz (map file in CCP4 format, 250001 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
400 pix
1.51 Å/pix.
= 604.8 Å
400 pix
1.51 Å/pix.
= 604.8 Å
400 pix
1.51 Å/pix.
= 604.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.512 Å
Density
Contour Level:0.25 (by author), 0.25 (movie #1):
Minimum - Maximum-0.61920553 - 0.88508433
Average (Standard dev.)0.00721371 (0.10529590)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions400400400
Origin-10-10-10
Limit389389389
Spacing400400400
CellA=B=C: 604.7999 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.5121.5121.512
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z604.800604.800604.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-10-10-10
NC/NR/NS400400400
D min/max/mean-0.6190.8850.007

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Supplemental data

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Sample components

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Entire 11 uM Cp183 dimer in capsid form and 18.8 uM Imp-beta in ammonium...

EntireName: 11 uM Cp183 dimer in capsid form and 18.8 uM Imp-beta in ammonium formate
Number of components: 2

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Component #1: virus, Hepatitis B virus

VirusName: Hepatitis B virus / a.k.a: HBV / Class: VIRUS-LIKE PARTICLE / Enveloped: No / Empty: No / Isolate: STRAIN
MassTheoretical: 4.8 MDa / Experimental: 4.8 MDa
SpeciesSpecies: Hepatitis B virus (HBV) / Strain: adyw
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: pET11cCp183 / Strain: BL21 (DE3) cells
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES
Shell #1Name of element: Cp183 / T number(triangulation number): 4

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Component #2: protein, importin beta

ProteinName: importin betaImportin / a.k.a: Imp-beta / Recombinant expression: Yes
SourceSpecies: Homo sapiens (human)
Source (engineered)Expression System: Escherichia coli (E. coli) / Vector: PET30a

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.39 mg/ml / Buffer solution: 0.15M NaCl, 10 mM DTT, 20 mM Tris-HCl / pH: 7.4
Support filmglow-discharged holey carbon grid (Quantifoil R2/2) or continuous carbon film coated grid (EMS)
VitrificationInstrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 98 K / Humidity: 100 % / Method: Blot for 4 seconds before plunging

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS / Date: Jun 19, 2014 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 80000 X (nominal) / Cs: 1.1 mm / Imaging mode: BRIGHT FIELD / Defocus: 1560 - 5460 nm / Energy filter: Omega filter / Energy window: 0-20 eV
Specimen HolderHolder: Gatan 626 / Model: GATAN LIQUID NITROGEN / Temperature: 98 K
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 129 / Sampling size: 15 microns

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 8365 / Details: Data processed by auto3dem
3D reconstructionSoftware: Auto3dem / CTF correction: each particle / Resolution: 10.1 Å / Resolution method: FSC at 0.143 cut-off

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