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- EMDB-47711: CPV2a capsid complexed with scFv2 -

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Basic information

Entry
Database: EMDB / ID: EMD-47711
TitleCPV2a capsid complexed with scFv2
Map dataA sharpened-map of CPV2a-scFv2 complex
Sample
  • Virus: Canine parvovirus 2a
    • Protein or peptide: Capsid protein
    • Protein or peptide: Light-chain of scFv clone 2
    • Protein or peptide: Heavy-chain of scFv clone 2
KeywordsVirus / Antibody / Complex / 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 speciesCanine parvovirus 2b / Canis lupus familiaris (dog) / Canine parvovirus 2a
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsLee H / Hafenstein S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Proc Natl Acad Sci U S A / Year: 2025
Title: Structures and functions of the limited natural polyclonal antibody response to parvovirus infection.
Authors: Oluwafemi F Adu / Hyunwook Lee / Simon P Früh / Marta V Schoenle / Wendy S Weichert / Andrew I Flyak / Susan L Hafenstein / Colin R Parrish /
Abstract: Host antibody responses are key components in the protection of animals against pathogens, yet the defining properties of viral antigens and induction of B cell responses that result in varied ...Host antibody responses are key components in the protection of animals against pathogens, yet the defining properties of viral antigens and induction of B cell responses that result in varied protection are still poorly understood. Parvoviruses are simple molecular structures that display 60 repeated motifs on their capsid surface, and rapidly induce strong antibody responses that protect animals from infection. We recently showed that following canine parvovirus infection of its natural host, the polyclonal response in the sera contained only two or three dominant antibodies that bound two epitopes on the capsid. Here, we characterize key antibodies present in that immune response, identifying their sequences, defining their binding properties on the capsid by cryoelectron microscopic (cryoEM) analysis, and testing their effects on viral infectivity. Two antibodies sharing the same heavy chain bound to the side of the capsid threefold spike (B-site), while another distinct antibody bound close to the threefold axis (A-site). The epitopes of these antibodies overlapped the binding site of the host receptor, the transferrin receptor type-1, but to varying degrees. The antibodies varied widely in their neutralization efficiencies as either immunoglobulins (IgGs) or monomeric antigen-binding fragments (Fabs), which was consistent with their ability to compete for the receptor. The monoclonal antibodies characterized here matched the structures from the cryoEM analysis of polyclonal sera, including those present in a different dog than the monoclonal source. This shows that after infection, a focused response to the viral antigen is produced that protects against infection.
History
DepositionNov 5, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47711.png

Downloads & links

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Map

FileDownload / File: emd_47711.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA sharpened-map of CPV2a-scFv2 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 448 pix.
= 430.08 Å		0.96 Å/pix.
x 448 pix.
= 430.08 Å		0.96 Å/pix.
x 448 pix.
= 430.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-0.14761664 - 2.1782858
Average (Standard dev.)0.010930469 (±0.080425665)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-224-224-224
Dimensions448448448
Spacing448448448
CellA=B=C: 430.08 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half-map A f the CPV2a-scFv2 complex

Fileemd_47711_half_map_1.map
AnnotationHalf-map A f the CPV2a-scFv2 complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map B of the CPV2a-scFv2 complex

Fileemd_47711_half_map_2.map
AnnotationHalf-map B of the CPV2a-scFv2 complex
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 2a

EntireName: Canine parvovirus 2a
Components
  • Virus: Canine parvovirus 2a
    • Protein or peptide: Capsid protein
    • Protein or peptide: Light-chain of scFv clone 2
    • Protein or peptide: Heavy-chain of scFv clone 2

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Supramolecule #1: Canine parvovirus 2a

SupramoleculeName: Canine parvovirus 2a / type: virus / ID: 1 / Parent: 0 / Macromolecule list: all / NCBI-ID: 497961 / Sci species name: Canine parvovirus 2a / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: Yes

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Macromolecule #1: Capsid protein

MacromoleculeName: Capsid protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canine parvovirus 2b
Molecular weightTheoretical: 64.745559 KDa
Recombinant expressionOrganism: Felis catus (domestic cat)
SequenceString: MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVY ITANSSRLVH LNMPESENYR RVVVNNLDK TAVNGNMALD DTHAEIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND ...String:
MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVY ITANSSRLVH LNMPESENYR RVVVNNLDK TAVNGNMALD DTHAEIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND LTASLMVALD SNNTMPFTPA AMRSETLGFY PWKPTIPTPW RYYFQWDRTL IPSHTGTSGT PTNIYHGTDP DD VQFYTIE NSVPVHLLRT GDEFATGTFF FDCKPCRLTH TWQTNRALGL PPFLNSLPQS EGGTNFGYIG VQQDKRRGVT QMG NTNYIT EATIMRPAEV GYSAPYYSFE ASTQGPFKTP IAAGRGGAQT DENQAADGDP RYAFGRQHGQ KTTTTGETPE RFTY IAHQD TGRYPEGDWI QNINFNLPVT DDNVLLPTDP IGGKTGINYT NIFNTYGPLT ALNNVPPVYP NGQIWDKEFD TDLKP RLHV NAPFVCQNNC PGQLFVKVAP NLTNQYDPDA SANMSRIVTY SDFWWKGKLV FKAKLRASHT WNPIQQMSIN VDNQFN YVP SNIGGMKIVY EKSQLAPRKL Y

UniProtKB: Capsid protein

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Macromolecule #2: Light-chain of scFv clone 2

MacromoleculeName: Light-chain of scFv clone 2 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 11.121105 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
VLTQKASVSG SLGQTITISC TGTSSNIGHN NVGWYQQLPG RGPRTVVSGT NSRPSGVSDR FSASKSGNTA TLTISGLRAD DEADYYCST WDDSLNVVFG GGTHLTVL

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Macromolecule #3: Heavy-chain of scFv clone 2

MacromoleculeName: Heavy-chain of scFv clone 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 14.165727 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString:
EVQLVESGGD LVKPGGSLRL SCEASGFTFS NYHMAWVRQA PGKGLQWVAN IDSGGFTTNY VDAVRGRFTV SRDNGALYLQ MNGLRVEDT AVYYCATMKT TYCIDENCNS FQAGRGVFDN WGQGTLVTVS S

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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
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.25 µm / Nominal defocus min: 0.75 µm
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 5253
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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