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- PDB-7utp: CPV Affinity Purified Polyclonal Fab A Site Fab -

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Basic information

Entry
Database: PDB / ID: 7utp
TitleCPV Affinity Purified Polyclonal Fab A Site Fab
Components
  • Capsid protein VP1
  • Heavy chain antibody fragment
  • Light chain antibody fragment
KeywordsVIRUS/IMMUNE SYSTEM / CPV / polyclonal Fab / A site / vaccination / VIRUS / VIRUS-IMMUNE SYSTEM complex
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 / microtubule-dependent intracellular transport of viral material towards nucleus / adhesion receptor-mediated virion attachment to host cell / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus / structural molecule activity / metal ion binding
Similarity search - Function
Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsHartmann, S.R. / Hafenstein, S.L. / Charnesky, A.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/Office of the DirectorS10OD026822-01 United States
National Institutes of Health/Office of the DirectorR01AI092571 United States
CitationJournal: Commun Biol / Year: 2023
Title: Cryo EM structures map a post vaccination polyclonal antibody response to canine parvovirus.
Authors: Samantha R Hartmann / Andrew J Charnesky / Simon P Früh / Robert A López-Astacio / Wendy S Weichert / Nadia DiNunno / Sung Hung Cho / Carol M Bator / Colin R Parrish / Susan L Hafenstein /
Abstract: Canine parvovirus (CPV) is an important pathogen that emerged by cross-species transmission to cause severe disease in dogs. To understand the host immune response to vaccination, sera from dogs ...Canine parvovirus (CPV) is an important pathogen that emerged by cross-species transmission to cause severe disease in dogs. To understand the host immune response to vaccination, sera from dogs immunized with parvovirus are obtained, the polyclonal antibodies are purified and used to solve the high resolution cryo EM structures of the polyclonal Fab-virus complexes. We use a custom software, Icosahedral Subparticle Extraction and Correlated Classification (ISECC) to perform subparticle analysis and reconstruct polyclonal Fab-virus complexes from two different dogs eight and twelve weeks post vaccination. In the resulting polyclonal Fab-virus complexes there are a total of five distinct Fabs identified. In both cases, any of the five antibodies identified would interfere with receptor binding. This polyclonal mapping approach identifies a specific, limited immune response to the live vaccine virus and allows us to investigate the binding of multiple different antibodies or ligands to virus capsids.
History
DepositionApr 27, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 4, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid protein VP1
L: Light chain antibody fragment
H: Heavy chain antibody fragment
G: Capsid protein VP1
F: Capsid protein VP1
D: Capsid protein VP1
E: Capsid protein VP1
I: Capsid protein VP1
C: Capsid protein VP1
B: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)510,15210
Polymers510,15210
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Capsid protein VP1 / / Coat protein VP1


Mass: 61562.367 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Canis lupus familiaris (dog) / Cell (production host): NLFK / Production host: Felis catus (domestic cat) / References: UniProt: Q11213
#2: Antibody Light chain antibody fragment


Mass: 8443.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
#3: Antibody Heavy chain antibody fragment


Mass: 9209.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus familiaris (dog)
Sequence detailsThe authors state that the sequences of the antibody fragments are unknown.

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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 in complex with polyclonal fab / Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES
Source (natural)Organism: Canis lupus familiaris (dog)
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 FIELDBright-field microscopy / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm
Image recordingElectron dose: 45 e/Å2 / Film or detector model: FEI FALCON III (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1-4487_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 11073540 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00731929
ELECTRON MICROSCOPYf_angle_d1.07843660
ELECTRON MICROSCOPYf_dihedral_angle_d6.8244237
ELECTRON MICROSCOPYf_chiral_restr0.0554764
ELECTRON MICROSCOPYf_plane_restr0.0095732

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