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- EMDB-2692: cryo-EM structure of Woodchuck Hepatitis Virus capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-2692
Titlecryo-EM structure of Woodchuck Hepatitis Virus capsid
Map dataCryo-EM 3-D reconstruction of Woodchuck Hepatitis Virus capsid
Sample
  • Sample: Woodchuck Hepatitis Virus core protein (wCp149)
  • Virus: Woodchuck hepatitis virus
KeywordsWoodchuck hepatitis virus / hepatitis B virus / cryo-EM / core protein
Biological speciesWoodchuck hepatitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.7 Å
AuthorsKukreja A / Wang Joesph C-Y / Pierson E / Keifer DZ / Dragnea B / Jarrold MF / Zlotnick A
CitationJournal: J Virol / Year: 2014
Title: Structurally similar woodchuck and human hepadnavirus core proteins have distinctly different temperature dependences of assembly.
Authors: Alexander A Kukreja / Joseph C-Y Wang / Elizabeth Pierson / David Z Keifer / Lisa Selzer / Zhenning Tan / Bogdan Dragnea / Martin F Jarrold / Adam Zlotnick /
Abstract: Woodchuck hepatitis virus (WHV), a close relative of human hepatitis B virus (HBV), has been a key model for disease progression and clinical studies. Sequences of the assembly domain of WHV and HBV ...Woodchuck hepatitis virus (WHV), a close relative of human hepatitis B virus (HBV), has been a key model for disease progression and clinical studies. Sequences of the assembly domain of WHV and HBV core proteins (wCp149 and hCp149, respectively) have 65% identity, suggesting similar assembly behaviors. We report a cryo-electron microscopy (cryo-EM) structure of the WHV capsid at nanometer resolution and characterization of wCp149 assembly. At this resolution, the T=4 capsid structures of WHV and HBV are practically identical. In contrast to their structural similarity, wCp149 demonstrates enhanced assembly kinetics and stronger dimer-dimer interactions than hCp149: at 23 °C and at 100 mM ionic strength, the pseudocritical concentrations of assembly of wCp149 and hCp149 are 1.8 μM and 43.3 μM, respectively. Transmission electron microscopy reveals that wCp149 assembles into predominantly T=4 capsids with a sizeable population of larger, nonicosahedral structures. Charge detection mass spectrometry indicates that T=3 particles are extremely rare compared to the ∼ 5% observed in hCp149 reactions. Unlike hCp149, wCp149 capsid assembly is favorable over a temperature range of 4 °C to 37 °C; van't Hoff analyses relate the differences in temperature dependence to the high positive values for heat capacity, enthalpy, and entropy of wCp149 assembly. Because the final capsids are so similar, these findings suggest that free wCp149 and hCp149 undergo different structural transitions leading to assembly. The difference in the temperature dependence of wCp149 assembly may be related to the temperature range of its hibernating host.
IMPORTANCE: In this paper, we present a cryo-EM structure of a WHV capsid showing its similarity to HBV. We then observe that the assembly properties of the two homologous proteins are very different. ...IMPORTANCE: In this paper, we present a cryo-EM structure of a WHV capsid showing its similarity to HBV. We then observe that the assembly properties of the two homologous proteins are very different. Unlike human HBV, the capsid protein of WHV has evolved to function in a nonhomeostatic environment. These studies yield insight into the interplay between core protein self-assembly and the host environment, which may be particularly relevant to plant viruses and viruses with zoonotic cycles involving insect vectors.
History
DepositionJun 24, 2014-
Header (metadata) releaseJul 9, 2014-
Map releaseNov 19, 2014-
UpdateDec 3, 2014-
Current statusDec 3, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.063
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.063
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2692.png

emd_2692.png

Downloads & links

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Map

FileDownload / File: emd_2692.map.gz / Format: CCP4 / Size: 101.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM 3-D reconstruction of Woodchuck Hepatitis Virus capsid
Voxel sizeX=Y=Z: 1.484 Å
Density
Contour LevelBy AUTHOR: 0.063 / Movie #1: 0.063
Minimum - Maximum-0.09766106 - 0.24926583
Average (Standard dev.)0.00249827 (±0.03142017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions301301301
Spacing301301301
CellA=B=C: 446.684 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.4841.4841.484
M x/y/z301301301
origin x/y/z0.0000.0000.000
length x/y/z446.684446.684446.684
α/β/γ90.00090.00090.000
start NX/NY/NZ-180-180-179
NX/NY/NZ360360360
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS301301301
D min/max/mean-0.0980.2490.002

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Supplemental data

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Sample components

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Entire : Woodchuck Hepatitis Virus core protein (wCp149)

EntireName: Woodchuck Hepatitis Virus core protein (wCp149)
Components
  • Sample: Woodchuck Hepatitis Virus core protein (wCp149)
  • Virus: Woodchuck hepatitis virus

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Supramolecule #1000: Woodchuck Hepatitis Virus core protein (wCp149)

SupramoleculeName: Woodchuck Hepatitis Virus core protein (wCp149) / type: sample / ID: 1000 / Oligomeric state: icosahedron / Number unique components: 1
Molecular weightTheoretical: 4.1 MDa

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Supramolecule #1: Woodchuck hepatitis virus

SupramoleculeName: Woodchuck hepatitis virus / type: virus / ID: 1
Details: WHV is an enveloped virus, but we present the truncated capsid structure here
NCBI-ID: 35269 / Sci species name: Woodchuck hepatitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: Yes
Host (natural)Organism: Marmota monax (woodchuck) / synonym: VERTEBRATES
Host systemOrganism: Escherichia coli (E. coli) / Recombinant strain: BL21 / Recombinant cell: E. coli cells / Recombinant plasmid: pET11c
Molecular weightExperimental: 4.1 MDa / Theoretical: 4.1 MDa
Virus shellShell ID: 1 / Name: capsid / 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

Concentration0.5 mg/mL
BufferpH: 7.5 / Details: 50 mM NaCl, 10 mM HEPES
GridDetails: Quantifoil R2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeJEOL 3200FS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 1.1 mm / Nominal defocus max: 0.0033 µm / Nominal defocus min: 0.0011 µm / Nominal magnification: 80000
Specialist opticsEnergy filter - Name: Omega / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
Sample stageSpecimen holder: 626 / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 97.15 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 80,000 times magnification
DetailsParallel weak beam illumination
DateDec 6, 2012
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Digitization - Sampling interval: 1.484 µm / Number real images: 133 / Average electron dose: 25 e/Å2 / Camera length: 250 / Details: Image is recorded on CCD

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: AUTO3DEM delta angle 0.7
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.7 Å / Resolution method: OTHER / Software - Name: AUTO3DEM / Number images used: 2254
DetailsParticles were boxed using e2boxer.py, defocus level was measured by CTFFIND3 and image processing was done by AUTO3DEM

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Atomic model buiding 1

Initial modelPDB ID:

1qgt


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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