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- EMDB-26789: CPV Total-Fab Polyclonal B Site Fab (1 of 2) -

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Basic information

Entry
Database: EMDB / ID: EMD-26789
TitleCPV Total-Fab Polyclonal B Site Fab (1 of 2)
Map data
Sample
  • Complex: Canine parvovirus in complex with antibody fragment
    • Protein or peptide: Light chain antibody fragment
    • Protein or peptide: Heavy chain antibody fragment
    • Protein or peptide: Capsid protein 2
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 / 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 speciesCanis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 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-
UpdateOct 30, 2024-
Current statusOct 30, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_26789.png

Downloads & links

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Map

FileDownload / File: emd_26789.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
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

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: 0.05
Minimum - Maximum-0.022107061 - 2.047867
Average (Standard dev.)0.00819744 (±0.057409413)
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_26789_additional_1.map
Projections & Slices
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Additional map: #1

Fileemd_26789_additional_2.map
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Half map: #2

Fileemd_26789_half_map_1.map
Projections & Slices
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Half map: #1

Fileemd_26789_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: Light chain antibody fragment
    • Protein or peptide: Heavy chain antibody fragment
    • Protein or peptide: Capsid protein 2

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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: Light chain antibody fragment

MacromoleculeName: Light chain antibody fragment / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 8.188084 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)

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Macromolecule #2: Heavy chain antibody fragment

MacromoleculeName: Heavy chain antibody fragment / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 9.719973 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)(UNK)(UNK)(UNK)(UNK)(UNK) (UNK) (UNK)

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Macromolecule #3: Capsid protein 2

MacromoleculeName: Capsid protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 8 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
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 2

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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

Startup modelType of model: OTHER / Details: ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 19370760
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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