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- EMDB-22643: Murine polyomavirus hexavalent capsomer, subparticle reconstruction -

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Basic information

Entry
Database: EMDB / ID: EMD-22643
TitleMurine polyomavirus hexavalent capsomer, subparticle reconstruction
Map dataMurine polyomavirus hexavalent capsomer, subparticle reconstruction
Sample
  • Virus: Murine polyomavirus strain A2
    • Protein or peptide: Capsid protein VP1
Keywordspolyomavirus / capsomer / VIRAL PROTEIN
Function / homology
Function and homology information


caveolin-mediated endocytosis of virus by host cell / T=7 icosahedral viral capsid / endocytosis involved in viral entry into host cell / virion attachment to host cell / host cell nucleus / structural molecule activity
Similarity search - Function
Capsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid
Similarity search - Domain/homology
Capsid protein VP1 / Capsid protein VP1
Similarity search - Component
Biological speciesMus musculus polyomavirus 1 / Murine polyomavirus strain A2
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 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 Neurological Disorders and Stroke (NIH/NINDS)R01NS092662 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)F32NS106730 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)F31NS083336 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 8, 2020-
Header (metadata) releaseOct 7, 2020-
Map releaseOct 7, 2020-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k25
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k25
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22643.png

Downloads & links

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Map

FileDownload / File: emd_22643.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMurine polyomavirus hexavalent capsomer, subparticle reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å		1.1 Å/pix.
x 300 pix.
= 330. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-23.310552999999999 - 30.466882999999999
Average (Standard dev.)0.000000001481236 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions300300300
Spacing300300300
CellA=B=C: 330.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z330.000330.000330.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ510510510
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
D min/max/mean-23.31130.4670.000

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Supplemental data

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Half map: Murine polyomavirus hexavalent capsomer, subparticle reconstruction

Fileemd_22643_half_map_1.map
AnnotationMurine polyomavirus hexavalent capsomer, subparticle reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Murine polyomavirus hexavalent capsomer, subparticle reconstruction

Fileemd_22643_half_map_2.map
AnnotationMurine polyomavirus hexavalent capsomer, subparticle reconstruction
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
    • Protein or peptide: Capsid protein VP1

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Supramolecule #1: Murine polyomavirus strain A2

SupramoleculeName: Murine polyomavirus strain A2 / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10636 / Sci species name: Murine polyomavirus strain A2 / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Virus shellShell ID: 1 / Diameter: 450.0 Å / T number (triangulation number): 7

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus polyomavirus 1
Molecular weightTheoretical: 42.493172 KDa
Recombinant expressionOrganism: Mus musculoides (Temminck's mouse)
SequenceString: APKRKSGVSK CETKCTKACP RPAPVPKLLI KGGMEVLDLV TGPDSVTEIE AFLNPRMGQP PTPESLTEGG QYYGWSRGIN LATSDTEDS PENNTLPTWS MAKLQLPMLN EDLTCDTLQM WEAVSVKTEV VGSGSLLDVH GFNKPTDTVN TKGISTPVEG S QYHVFAVG ...String:
APKRKSGVSK CETKCTKACP RPAPVPKLLI KGGMEVLDLV TGPDSVTEIE AFLNPRMGQP PTPESLTEGG QYYGWSRGIN LATSDTEDS PENNTLPTWS MAKLQLPMLN EDLTCDTLQM WEAVSVKTEV VGSGSLLDVH GFNKPTDTVN TKGISTPVEG S QYHVFAVG GEPLDLQGLV TDARTKYKEE GVVTIKTITK KDMVNKDQVL NPISKAKLDK DGMYPVEIWH PDPAKNENTR YF GNYTGGT TTPPVLQFTN TLTTVLLDEN GVGPLCKGEG LYLSCVDIMG WRVTRNYDVH HWRGLPRYFK ITLRKRWVKN PYP MASLIS SLFNNMLPQV QGQPMEGENT QVEEVRVYDG TEPVPGDPDM TRYVDRFGKT KTVFPGN

UniProtKB: Capsid protein VP1

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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
Component:
ConcentrationFormula
10.0 mMHEPES
1.0 mMCaCl2
1.0 mMMgCl2
5.0 mMKCl

Details: 10 mM HEPES pH 7.9, 1 mM CaCl2, 1 mM MgCl2, 5 mM KCl
VitrificationCryogen name: ETHANE / Chamber humidity: 95 %
DetailsMuPyV (2.8 mg/mL)

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Electron microscopy

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

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Image processing

Startup modelType of model: INSILICO MODEL
In silico model: Initial model generated ab initio in cryoSPARC with I1 symmetry imposed. Initial model for subvolume reconstruction was generated using 10,000 subparticles using ISECC_subpaticle_extract.
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 929940
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Details: I1-constrained angles for whole capsid derived using 3D Refinement in RELION. Subparticle initial angles and offsets were mathematically derived from icosahedral parameters using ISECC_subpaticle_extract.
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Details: Local search for angles and offsets in RELION from the icosahedrally-derived subparticle parameters.
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1sie

source_name: PDB, initial_model_type: experimental model

3gk8

source_name: PDB, initial_model_type: experimental model
DetailsHomology model for Fab was generated using SwissModel. Initial models were docked into density in Chimera. Fab CDR loops were manually rebuilt in Coot. Iterative rounds of real space refinements (PHENIX) and manual adjustment (coot) were conducted to improve fit to density.
RefinementSpace: REAL
Output model

PDB-7k25:
Murine polyomavirus hexavalent capsomer, subparticle reconstruction

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