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- PDB-7m3o: Canine parvovirus asymmetric map -

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Basic information

Entry
Database: PDB / ID: 7m3o
TitleCanine parvovirus asymmetric map
ComponentsCapsid protein 2
KeywordsVIRUS / canine parvovirus / CPV / Fab14 / Cryo EM
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host 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 speciesCanine parvovirus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å
AuthorsGoteschius, D.J. / Hartmann, S.R. / Hafenstein, S.L.
Funding support United States, 1items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release

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Structure visualization

Movie
  • Biological unit as complete icosahedral assembly
  • Imaged by Jmol
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
  • EMDB-23659
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  • Superimposition on EM map
  • EMDB-23659
  • Imaged by UCSF Chimera
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein 2


Theoretical massNumber of molelcules
Total (without water)64,7061
Polymers64,7061
Non-polymers00
Water00
1
A: Capsid protein 2
x 60


Theoretical massNumber of molelcules
Total (without water)3,882,33460
Polymers3,882,33460
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: Capsid protein 2
x 5


  • icosahedral pentamer
  • 324 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)323,5285
Polymers323,5285
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: Capsid protein 2
x 6


  • icosahedral 23 hexamer
  • 388 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)388,2336
Polymers388,2336
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein 2 / VP2


Mass: 64705.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canine parvovirus type 2 / Production host: Canine parvovirus / References: UniProt: B2ZG07

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Canine parvovirus / Type: VIRUS / Entity ID: all / Source: NATURAL
Source (natural)Organism: Canine parvovirus
Details of virusEmpty: NO / Enveloped: NO / Isolate: SPECIES / Type: VIRION
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.17.1-3660_3260: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 162627
Details: Asymmetric reconstruction, particle number is 162,627*10.2 orientations per particle
Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0114363
ELECTRON MICROSCOPYf_angle_d0.725966
ELECTRON MICROSCOPYf_dihedral_angle_d9.454573
ELECTRON MICROSCOPYf_chiral_restr0.052643
ELECTRON MICROSCOPYf_plane_restr0.006785

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