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- EMDB-22646: Murine polyomavirus with 8A7H5 Fab (icosahedral reconstruction) -

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Basic information

Entry
Database: EMDB / ID: EMD-22646
TitleMurine polyomavirus with 8A7H5 Fab (icosahedral reconstruction)
Map datasharpened map, icosahedrally refined, cropped to 700 box
Sample
  • Virus: Murine polyomavirus strain A2
Biological speciesMurine polyomavirus strain A2
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsGoetschius DJ / Hafenstein SL
Funding support United States, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS088367 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI107121 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)R01NS092662 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS083336 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F32NS106730 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)T32CA060395 United States
CitationJournal: Elife / Year: 2020
Title: Antibody escape by polyomavirus capsid mutation facilitates neurovirulence.
Authors: Matthew D Lauver / Daniel J Goetschius / Colleen S Netherby-Winslow / Katelyn N Ayers / Ge Jin / Daniel G Haas / Elizabeth L Frost / Sung Hyun Cho / Carol M Bator / Stephanie M Bywaters / ...Authors: Matthew D Lauver / Daniel J Goetschius / Colleen S Netherby-Winslow / Katelyn N Ayers / Ge Jin / Daniel G Haas / Elizabeth L Frost / Sung Hyun Cho / Carol M Bator / Stephanie M Bywaters / Neil D Christensen / Susan L Hafenstein / Aron E Lukacher /
Abstract: JCPyV polyomavirus, a member of the human virome, causes progressive multifocal leukoencephalopathy (PML), an oft-fatal demyelinating brain disease in individuals receiving immunomodulatory therapies. ...JCPyV polyomavirus, a member of the human virome, causes progressive multifocal leukoencephalopathy (PML), an oft-fatal demyelinating brain disease in individuals receiving immunomodulatory therapies. Mutations in the major viral capsid protein, VP1, are common in JCPyV from PML patients (JCPyV-PML) but whether they confer neurovirulence or escape from virus-neutralizing antibody (nAb) in vivo is unknown. A mouse polyomavirus (MuPyV) with a sequence-equivalent JCPyV-PML VP1 mutation replicated poorly in the kidney, a major reservoir for JCPyV persistence, but retained the CNS infectivity, cell tropism, and neuropathology of the parental virus. This mutation rendered MuPyV resistant to a monoclonal Ab (mAb), whose specificity overlapped the endogenous anti-VP1 response. Using cryo-EM and a custom sub-particle refinement approach, we resolved an MuPyV:Fab complex map to 3.2 Å resolution. The structure revealed the mechanism of mAb evasion. Our findings demonstrate convergence between nAb evasion and CNS neurovirulence in vivo by a frequent JCPyV-PML VP1 mutation.
History
DepositionSep 9, 2020-
Header (metadata) releaseSep 23, 2020-
Map releaseSep 23, 2020-
UpdateOct 28, 2020-
Current statusOct 28, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22646.png

Downloads & links

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Map

FileDownload / File: emd_22646.map.gz / Format: CCP4 / Size: 1.3 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened map, icosahedrally refined, cropped to 700 box
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.3 / Movie #1: 0.3
Minimum - Maximum-0.8277897 - 1.4232649
Average (Standard dev.)0.007587357 (±0.12717277)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions700700700
Spacing700700700
CellA=B=C: 770.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z700700700
origin x/y/z0.0000.0000.000
length x/y/z770.000770.000770.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS700700700
D min/max/mean-0.8281.4230.008

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Supplemental data

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Half map: Halfmap. icosahedrally refined, cropped to 700 box

Fileemd_22646_half_map_1.map
AnnotationHalfmap. icosahedrally refined, cropped to 700 box
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Halfmap. icosahedrally refined, cropped to 700 box

Fileemd_22646_half_map_2.map
AnnotationHalfmap. icosahedrally refined, cropped to 700 box
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Murine polyomavirus strain A2

EntireName: Murine polyomavirus strain A2
Components
  • Virus: Murine polyomavirus strain A2

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Supramolecule #1: Murine polyomavirus strain A2

SupramoleculeName: Murine polyomavirus strain A2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1
Details: MuPyV (2.8 mg/mL) was incubated with 8A7H5 Fab (1.1 mg/mL) for 30 m at room temperature
NCBI-ID: 10636 / Sci species name: Murine polyomavirus strain A2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host systemOrganism: Mus musculoides (Temminck's mouse)
Virus shellShell ID: 1 / Diameter: 450.0 Å / T number (triangulation number): 7

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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

Concentration2.8 mg/mL
BufferpH: 7.9
Details: 10 mM HEPES pH 7.9, 1 mM CaCl2, 1 mM MgCl2, 5 mM KCl
VitrificationCryogen name: ETHANE
DetailsMuPyV (2.8 mg/mL)

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Number grids imaged: 1 / Average electron dose: 45.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC
Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated ab initio in cryoSPARC
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 9146

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