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- EMDB-9031: Cryo-EM structure of Woodchuck hepatitis virus capsid -

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Basic information

Entry
Database: EMDB / ID: EMD-9031
TitleCryo-EM structure of Woodchuck hepatitis virus capsid
Map dataWoodchuck hepatitis virus capsid
Sample
  • Virus: Woodchuck hepatitis virus
    • Protein or peptide: External core antigen
KeywordsWHV / Capsid structure / VIRUS LIKE PARTICLE
Function / homology
Function and homology information


virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity ...virus-mediated perturbation of host defense response => GO:0019049 / microtubule-dependent intracellular transport of viral material towards nucleus / T=4 icosahedral viral capsid / : / virus-mediated perturbation of host defense response / viral penetration into host nucleus / host cell cytoplasm / symbiont entry into host cell / host cell nucleus / structural molecule activity / DNA binding / RNA binding / extracellular region
Similarity search - Function
Hepatitis B virus, capsid N-terminal / Hepatitis core protein, putative zinc finger / Hepatitis core antigen / Viral capsid core domain supefamily, Hepatitis B virus / Hepatitis core antigen
Similarity search - Domain/homology
External core antigen / External core antigen
Similarity search - Component
Biological speciesWoodchuck hepatitis virus
Methodsingle particle reconstruction / cryo EM / Resolution: 4.52 Å
AuthorsZhao Z / Wang JC
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01-AI11893 United States
CitationJournal: J Virol / Year: 2019
Title: Structural Differences between the Woodchuck Hepatitis Virus Core Protein in the Dimer and Capsid States Are Consistent with Entropic and Conformational Regulation of Assembly.
Authors: Zhongchao Zhao / Joseph Che-Yen Wang / Giovanni Gonzalez-Gutierrez / Balasubramanian Venkatakrishnan / Roi Asor / Daniel Khaykelson / Uri Raviv / Adam Zlotnick /
Abstract: Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), ...Hepadnaviruses are hepatotropic enveloped DNA viruses with an icosahedral capsid. Hepatitis B virus (HBV) causes chronic infection in an estimated 240 million people; woodchuck hepatitis virus (WHV), an HBV homologue, has been an important model system for drug development. The dimeric capsid protein (Cp) has multiple functions during the viral life cycle and thus has become an important target for a new generation of antivirals. Purified HBV and WHV Cp spontaneously assemble into 120-dimer capsids. Though they have 65% identity, WHV Cp has error-prone assembly with stronger protein-protein association. We have taken advantage of the differences in assemblies to investigate the basis of assembly regulation. We determined the structures of the WHV capsid to 4.5-Å resolution by cryo-electron microscopy (cryo-EM) and of the WHV Cp dimer to 2.9-Å resolution by crystallography and examined the biophysical properties of the dimer. We found, in dimer, that the subdomain that makes protein-protein interactions is partially disordered and rotated 21° from its position in capsid. This subdomain is susceptible to proteolysis, consistent with local disorder. WHV assembly shows similar susceptibility to HBV antiviral molecules, suggesting that HBV assembly follows similar transitions. These data show that there is an entropic cost for assembly that is compensated for by the energetic gain of burying hydrophobic interprotein contacts. We propose a series of stages in assembly that incorporate a disorder-to-order transition and structural shifts. We suggest that a cascade of structural changes may be a common mechanism for regulating high-fidelity capsid assembly in HBV and other viruses. Virus capsids assemble spontaneously with surprisingly high fidelity. This requires strict geometry and a narrow range of association energies for these protein-protein interactions. It was hypothesized that requiring subunits to undergo a conformational change to become assembly active could regulate assembly by creating an energetic barrier and attenuating association. We found that woodchuck hepatitis virus capsid protein undergoes structural transitions between its dimeric and its 120-dimer capsid states. It is likely that the closely related hepatitis B virus capsid protein undergoes similar structural changes, which has implications for drug design. Regulation of assembly by structural transition may be a common mechanism for many viruses.
History
DepositionAug 9, 2018-
Header (metadata) releaseSep 5, 2018-
Map releaseMay 1, 2019-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6edj
  • Surface level: 0.0314
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-6edj
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9031.png

Downloads & links

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Map

FileDownload / File: emd_9031.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWoodchuck hepatitis virus capsid
Voxel sizeX=Y=Z: 1.72 Å
Density
Contour LevelBy AUTHOR: 0.0314 / Movie #1: 0.0314
Minimum - Maximum-0.073127106 - 0.100521594
Average (Standard dev.)0.00039009104 (±0.0061770887)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 516.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.721.721.72
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z516.000516.000516.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-0.0730.1010.000

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Supplemental data

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Mask #1

Fileemd_9031_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Woodchuck hepatitis virus

EntireName: Woodchuck hepatitis virus
Components
  • Virus: Woodchuck hepatitis virus
    • Protein or peptide: External core antigen

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Supramolecule #1: Woodchuck hepatitis virus

SupramoleculeName: Woodchuck hepatitis virus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 35269 / Sci species name: Woodchuck hepatitis virus / Virus type: VIRUS-LIKE PARTICLE / Virus isolate: OTHER / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: External core antigen

MacromoleculeName: External core antigen / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Woodchuck hepatitis virus
Molecular weightTheoretical: 17.126465 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MDIDPYKEFG SSYQLLNFLP LDFFPDLNAL VDTATALYEE ELTGREHCSP HHTAIRQALV CWDELTKLIA WMSSNITSEQ VRTIIVNHV NDTWGLKVRQ SLWFHLSCLT FGQHTVQEFL VSFGVWIRTP APYRPPNAPI LSTLPEHTVI

UniProtKB: External core antigen

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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

Concentration10 mg/mL
BufferpH: 7.5
GridDetails: unspecified
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Resolution.type: BY AUTHOR / Resolution: 4.52 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 7911
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ecs


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-6edj:
Cryo-EM structure of Woodchuck hepatitis virus capsid

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