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- EMDB-26787: CPV Affinity Purified Polyclonal Fab B Site Fab -

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Basic information

Entry
Database: EMDB / ID: EMD-26787
TitleCPV Affinity Purified Polyclonal Fab B Site Fab
Map data
Sample
  • Complex: Canine parvovirus in complex with antibody fragment
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Light chain antibody fragment
    • Protein or peptide: Heavy chain antibody fragment
KeywordsCPV / polyclonal Fab / B site / vaccination / VIRUS / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont entry into host cell via permeabilization of host 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 / host cell / 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 VP1/VP2 / Capsid/spike protein, ssDNA virus
Similarity search - Domain/homology
Biological speciesCanis lupus familiaris (dog) / Canine parvovirus type 2 (isolate Dog/United States/CPV-b/1978)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsHartmann SR / Hafenstein SL / Charnesky AJ
Funding support United States, 2 items
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, 2022-
Header (metadata) releaseOct 4, 2023-
Map releaseOct 4, 2023-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26787.png

Downloads & links

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Map

FileDownload / File: emd_26787.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å		1.1 Å/pix.
x 200 pix.
= 220. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05
Minimum - Maximum-0.012906418 - 2.1461978
Average (Standard dev.)0.012430916 (±0.0819995)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-100-100-100
Dimensions200200200
Spacing200200200
CellA=B=C: 220.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: #2

Fileemd_26787_additional_1.map
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Additional map: #1

Fileemd_26787_additional_2.map
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Half map: #2

Fileemd_26787_half_map_1.map
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Half map: #1

Fileemd_26787_half_map_2.map
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Sample components

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Entire : Canine parvovirus in complex with antibody fragment

EntireName: Canine parvovirus in complex with antibody fragment
Components
  • Complex: Canine parvovirus in complex with antibody fragment
    • Protein or peptide: Capsid protein VP1
    • Protein or peptide: Light chain antibody fragment
    • Protein or peptide: Heavy chain antibody fragment

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Supramolecule #1: Canine parvovirus in complex with antibody fragment

SupramoleculeName: Canine parvovirus in complex with antibody fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Canis lupus familiaris (dog)

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Macromolecule #1: Capsid protein VP1

MacromoleculeName: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Canine parvovirus type 2 (isolate Dog/United States/CPV-b/1978)
Strain: isolate Dog/United States/CPV-b/1978
Molecular weightTheoretical: 61.562367 KDa
Recombinant expressionOrganism: Felis catus (domestic cat)
SequenceString: GVGISTGTFN NQTEFKFLEN GWVEITANSS RLVHLNMPES ENYRRVVVNN MDKTAVNGNM ALDDIHAQIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI ...String:
GVGISTGTFN NQTEFKFLEN GWVEITANSS RLVHLNMPES ENYRRVVVNN MDKTAVNGNM ALDDIHAQIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI PTPWRYYFQW DRTLIPSHTG TSGTPTNIYH GTDPDDVQFY TIENSVPVHL LRTGDEFATG TFFFDCKPCR LT HTWQTNR ALGLPPFLNS LPQSEGATNF GDIGVQQDKR RGVTQMGNTN YITEATIMRP AEVGYSAPYY SFEASTQGPF KTP IAAGRG GAQTDENQAA DGNPRYAFGR QHGQKTTTTG ETPERFTYIA HQDTGRYPEG DWIQNINFNL PVTNDNVLLP TDPI GGKTG INYTNIFNTY GPLTALNNVP PVYPNGQIWD KEFDTDLKPR LHVNAPFVCQ NNCPGQLFVK VAPNLTNEYD PDASA NMSR IVTYSDFWWK GKLVFKAKLR ASHTWNPIQQ MSINVDNQFN YVPSNIGGMK IVYEKSQLAP RKLY

UniProtKB: Capsid protein VP1

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Macromolecule #2: Light chain antibody fragment

MacromoleculeName: Light chain antibody fragment / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 8.102979 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)

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Macromolecule #3: Heavy chain antibody fragment

MacromoleculeName: Heavy chain antibody fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 9.124238 KDa
SequenceString: (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) ...String:
(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK)(UNK)(UNK)

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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
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: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11073540
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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