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- EMDB-23657: Canine parvovirus and Fab14 at partial occupancy -

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Basic information

Entry
Database: EMDB / ID: EMD-23657
TitleCanine parvovirus and Fab14 at partial occupancy
Map dataCanine parvovirus and Fab14 at partial occupancy
Sample
  • Virus: Canine parvovirus
    • Protein or peptide: Capsid protein 2
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / T=1 icosahedral viral capsid / clathrin-dependent endocytosis of virus by host cell / virion attachment to host cell / structural molecule activity
Similarity search - Function
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCPV-2 (virus) / Canine parvovirus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.26 Å
AuthorsGoteschius DJ / Hartmann SR / Hafenstein SL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10RR031780 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2021
Title: High-resolution asymmetric structure of a Fab-virus complex reveals overlap with the receptor binding site.
Authors: Daniel J Goetschius / Samantha R Hartmann / Lindsey J Organtini / Heather Callaway / Kai Huang / Carol M Bator / Robert E Ashley / Alexander M Makhov / James F Conway / Colin R Parrish / Susan L Hafenstein /
Abstract: Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids ...Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site has contributed to cross-species transmission, giving rise to closely related variants. It has been shown that Mab 14 strongly binds and neutralizes canine but not feline parvovirus, suggesting this antigenic site also controls species-specific receptor binding. To visualize the conformational epitope at high resolution, we solved the cryogenic electron microscopy (cryo-EM) structure of the Fab-virus complex. We also created custom software, Icosahedral Subparticle Extraction and Correlated Classification, to solve a Fab-virus complex with only a few Fab bound per capsid and visualize local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex map. Our results identified the antigenic epitope that had significant overlap with the receptor binding site, and the structures revealed that binding of Fab induced conformational changes to the virus. We were also able to assign the order and position of attached Fabs to allow assessment of complementarity between the Fabs bound to different positions. This approach therefore provides a method for using cryo-EM to investigate complementarity of antibody binding.
History
DepositionMar 18, 2021-
Header (metadata) releaseJul 28, 2021-
Map releaseJul 28, 2021-
UpdateJul 28, 2021-
Current statusJul 28, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7m3m
  • Surface level: 0.2
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7m3m
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_23657.png

Downloads & links

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Map

FileDownload / File: emd_23657.map.gz / Format: CCP4 / Size: 371.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCanine parvovirus and Fab14 at partial occupancy
Voxel sizeX=Y=Z: 1.1 Å
Density
Contour LevelBy AUTHOR: 0.2 / Movie #1: 0.2
Minimum - Maximum-0.037197795 - 1.5619497
Average (Standard dev.)0.004701251 (±0.046558302)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-230-230-230
Dimensions460460460
Spacing460460460
CellA=B=C: 506.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.11.11.1
M x/y/z460460460
origin x/y/z0.0000.0000.000
length x/y/z506.000506.000506.000
α/β/γ90.00090.00090.000
start NX/NY/NZ1331310
NX/NY/NZ223226424
MAP C/R/S123
start NC/NR/NS-230-230-230
NC/NR/NS460460460
D min/max/mean-0.0371.5620.005

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Supplemental data

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Half map: Half-map 1

Fileemd_23657_half_map_1.map
AnnotationHalf-map 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2

Fileemd_23657_half_map_2.map
AnnotationHalf-map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Canine parvovirus

EntireName: Canine parvovirus
Components
  • Virus: Canine parvovirus
    • Protein or peptide: Capsid protein 2

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Supramolecule #1: Canine parvovirus

SupramoleculeName: Canine parvovirus / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 10788 / Sci species name: Canine parvovirus / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No

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Macromolecule #1: Capsid protein 2

MacromoleculeName: Capsid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: CPV-2 (virus)
Molecular weightTheoretical: 64.705559 KDa
SequenceString: MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVE ITANSSRLVH LNMPESENYR RVVVNNMDK TAVNGNMALD DIHAQIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND ...String:
MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVE ITANSSRLVH LNMPESENYR RVVVNNMDK TAVNGNMALD DIHAQIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND LTASLMVALD SNNTMPFTPA AMRSETLGFY PWKPTIPTPW RYYFQWDRTL IPSHTGTSGT PTNIYHGTDP DD VQFYTIE NSVPVHLLRT GDEFATGTFF FDCKPCRLTH TWQTNRALGL PPFLNSLPQS EGATNFGDIG VQQDKRRGVT QMG NTNYIT EATIMRPAEV GYSAPYYSFE ASTQGPFKTP IAAGRGGAQT DENQAADGNP RYAFGRQHGQ KTTTTGETPE RFTY IAHQD TGRYPEGDWI QNINFNLPVT NDNVLLPTDP IGGKTGINYT NIFNTYGPLT ALNNVPPVYP NGQIWDKEFD TDLKP RLHV NAPFVCQNNC PGQLFVKVAP NLTNEYDPDA SANMSRIVTY SDFWWKGKLV FKAKLRASHT WNPIQQMSIN VDNQFN YVP SNIGGMKIVY EKSQLAPRKL Y

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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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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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: FEI FALCON III (4k x 4k) / Average electron dose: 60.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.26 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 162627

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