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- EMDB-0272: F97L Hepatitis B core protein capsid -

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Basic information

Entry
Database: EMDB / ID: 0272
TitleF97L Hepatitis B core protein capsid
Map data
SampleHepatitis B virus:
virus / Capsid proteinCapsid
Function / homologyViral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Hepatitis core antigen / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / structural molecule activity ...Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen / Hepatitis core antigen / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / viral penetration into host nucleus / viral entry into host cell / host cell cytoplasm / pathogenesis / structural molecule activity / RNA binding / DNA binding / Capsid protein
Function and homology information
SourceHepatitis B virus
Methodsingle particle reconstruction / cryo EM / 2.64 Å resolution
AuthorsBottcher B / Nassal M
CitationJournal: J. Mol. Biol. / Year: 2018
Title: Structure of Mutant Hepatitis B Core Protein Capsids with Premature Secretion Phenotype.
Authors: Bettina Böttcher / Michael Nassal
Abstract: Hepatitis B virus is a major human pathogen that consists of a viral genome surrounded by an icosahedrally ordered core protein and a polymorphic, lipidic envelope that is densely packed with surface ...Hepatitis B virus is a major human pathogen that consists of a viral genome surrounded by an icosahedrally ordered core protein and a polymorphic, lipidic envelope that is densely packed with surface proteins. A point mutation in the core protein in which a phenylalanine at position 97 is exchanged for a smaller leucine leads to premature envelopment of the capsid before the genome maturation is fully completed. We have used electron cryo-microscopy and image processing to investigate how the point mutation affects the structure of the capsid at 2.6- to 2.8 Å-resolution. We found that in the mutant the smaller side chain at position 97 is displaced, increasing the size of an adjacent pocket in the center of the spikes of the capsid. In the mutant, this pocket is filled with an unknown density. Phosphorylation of serine residues in the unresolved C-terminal domain of the mutant leaves the structure of the ordered capsid largely unchanged. However, we were able to resolve several previously unresolved residues downstream of proline 144 that precede the phosphorylation-sites. These residues pack against the neighboring subunits and increase the inter-dimer contact suggesting that the C-termini play an important role in capsid stabilization and provide a much larger interaction interface than previously observed.
Validation ReportPDB-ID: 6hu4

SummaryFull reportAbout validation report
DateDeposition: Oct 5, 2018 / Header (metadata) release: Dec 26, 2018 / Map release: Dec 26, 2018 / Last update: Dec 26, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6hu4
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic models: PDB-6hu4
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_0272.map.gz (map file in CCP4 format, 536871 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
512 pix
1.05 Å/pix.
= 539.136 Å
512 pix
1.05 Å/pix.
= 539.136 Å
512 pix
1.05 Å/pix.
= 539.136 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.053 Å
Density
Contour Level:0.025 (by author), 0.025 (movie #1):
Minimum - Maximum-0.010896593 - 0.03513043
Average (Standard dev.)0.0002746374 (0.002324411)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions512512512
Origin0.00.00.0
Limit511.0511.0511.0
Spacing512512512
CellA=B=C: 539.136 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0531.0531.053
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z539.136539.136539.136
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS512512512
D min/max/mean-0.1420.2520.001

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Supplemental data

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Mask #1

Fileemd_0272_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire Hepatitis B virus

EntireName: Hepatitis B virus / Number of components: 2

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Component #1: virus, Hepatitis B virus

VirusName: Hepatitis B virus / Class: VIRUS-LIKE PARTICLE / Empty: No / Enveloped: No / Isolate: STRAIN
MassTheoretical: 4.8 MDa
SpeciesSpecies: Hepatitis B virus
Source (engineered)Expression System: Escherichia coli (E. coli)
Source (natural)Host Species: Hepatitis B virus / Host species strain: ayw
Shell #1Name of element: WT Hbc / Diameter: 340.0 Å / T number(triangulation number): 4

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Component #2: protein, Capsid protein

ProteinName: Capsid proteinCapsid
Details: Hepatitis B core protein premature envelopment mutant F97L
Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 21.112199 kDa
SourceSpecies: Hepatitis B virus
Source (engineered)Expression System: Escherichia coli (E. coli)

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 5 mg/ml / Buffer solution: 25 mM Tris pH 7.7, 150 mM NaCl / pH: 7.7
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 4 K / Humidity: 100 %
Details: Samples were vitrified with an FEI Vitrobot IV, which was operated at 100% humidity at 4C. 2.5-3.5 ul of sample were applied to grids (Quantifoil UltrAuFoil R1.3/1.2 300 mesh gold grids ) that were glow discharged in air for 1-2 min. The sample was incubated for 30 s before blotting for 3 s with a blot force between 0 and 5..

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 28 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 75000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Energy filter: GIF Quantum LS
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 1948

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: I (icosahedral) / Number of projections: 38292
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 2.64 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL
Input PDB model: 6HTX
Overall bvalue: 85
Output model

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