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- EMDB-22640: Murine polyomavirus pentavalent capsomer with 8A7H5 Fab, subparti... -

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Basic information

Entry
Database: EMDB / ID: EMD-22640
TitleMurine polyomavirus pentavalent capsomer with 8A7H5 Fab, subparticle reconstruction
Map dataPostprocessed map of locally-refined pentavalent capsomer w/ Fab
Sample
  • Complex: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1
    • Complex: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain
      • Protein or peptide: 8A7H5 Fab light chain
      • Protein or peptide: 8A7H5 Fab heavy chain
    • Complex: Capsid protein VP1
      • Protein or peptide: Capsid protein VP1
Keywordspolyomavirus / capsomer / VIRAL PROTEIN
Function / homologyCapsid protein VP1,Polyomavirus / Polyomavirus capsid protein VP1 superfamily / Polyomavirus coat protein / Double-stranded DNA virus, group I, capsid / T=7 icosahedral viral capsid / host cell nucleus / virion attachment to host cell / structural molecule activity / Capsid protein VP1
Function and homology information
Biological speciesRattus norvegicus (Norway rat) / Murine polyomavirus strain A2 / Mus musculus polyomavirus 1
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 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-
UpdateNov 6, 2024-
Current statusNov 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 2.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7k22
  • Surface level: 2.5
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7k22
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22640.png

Downloads & links

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Map

FileDownload / File: emd_22640.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of locally-refined pentavalent capsomer w/ Fab
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: 2.5 / Movie #1: 2.5
Minimum - Maximum-18.109148000000001 - 24.311886000000001
Average (Standard dev.)-0.000000000699257 (±0.99999994)
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-18.10924.312-0.000

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Supplemental data

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Half map: Unfiltered halfmap

Fileemd_22640_half_map_1.map
AnnotationUnfiltered halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Unfiltered halfmap

Fileemd_22640_half_map_2.map
AnnotationUnfiltered halfmap
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1

EntireName: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1
Components
  • Complex: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1
    • Complex: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain
      • Protein or peptide: 8A7H5 Fab light chain
      • Protein or peptide: 8A7H5 Fab heavy chain
    • Complex: Capsid protein VP1
      • Protein or peptide: Capsid protein VP1

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Supramolecule #1: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1

SupramoleculeName: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain, Capsid protein VP1
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Fab fragment generated from rat IgG

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Supramolecule #2: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain

SupramoleculeName: 8A7H5 Fab light chain, 8A7H5 Fab heavy chain / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: Rattus norvegicus (Norway rat)

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Supramolecule #3: Capsid protein VP1

SupramoleculeName: Capsid protein VP1 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3
Source (natural)Organism: Murine polyomavirus strain A2

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Macromolecule #1: 8A7H5 Fab light chain

MacromoleculeName: 8A7H5 Fab light chain / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 12.086437 KDa
SequenceString:
DIVMTQSPTS MSISVGDRVT MNCRASQNVY SNVDWYQQKT GQSPKLVIYK ASNRYTGVPD RFTGSGSGTY FTLTITNIQT EDLAVYYCL QSNAFPFTFG SGTKLETTRA

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Macromolecule #2: 8A7H5 Fab heavy chain

MacromoleculeName: 8A7H5 Fab heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Rattus norvegicus (Norway rat)
Molecular weightTheoretical: 13.217701 KDa
SequenceString:
EESGGGLVQP GKSLKLSCSA SGFTFSSYGM HWIRQVPGKG LDWVAYISSA SDTFYADAVK ERFTISRDNA KNTLYLRLNS LKSEDTAIY YCARTRYPTD HFYDWFPYWG QGTLVTVS

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Macromolecule #3: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 3 / 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
Details: 10 mM HEPES pH 7.9, 1 mM CaCl2, 1 mM MgCl2, 5 mM KCl
VitrificationCryogen name: ETHANE
DetailsMuPyV (2.8 mg/mL) was incubated with 8A7H5 Fab (1.1 mg/mL) for 30 m at room temperature

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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: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 109752
Initial angle assignmentType: MAXIMUM LIKELIHOOD
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
FSC plot (resolution estimation)

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