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- EMDB-47694: Canine parvovirus subtype 2a empty capsid in complex with Fab fra... -

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Basic information

Entry
Database: EMDB / ID: EMD-47694
TitleCanine parvovirus subtype 2a empty capsid in complex with Fab fragments of Mab 2C5
Map dataA sharpened asymmetric map of the CPV2a-Fab 2C5 complex
Sample
  • Virus: Canine parvovirus 2a
    • Protein or peptide: Capsid protein 2
    • Protein or peptide: Heavy chain antibody fragment
    • Protein or peptide: Light chain antibody fragment
KeywordsVirus / Antibody / 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 2a / Canis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 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 4, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMay 14, 2025-
Current statusMay 14, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47694.png

Downloads & links

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Map

FileDownload / File: emd_47694.map.gz / Format: CCP4 / Size: 775.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationA sharpened asymmetric map of the CPV2a-Fab 2C5 complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 588 pix.
= 492.156 Å		0.84 Å/pix.
x 588 pix.
= 492.156 Å		0.84 Å/pix.
x 588 pix.
= 492.156 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.837 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.1
Minimum - Maximum-0.09667874 - 2.0542219
Average (Standard dev.)0.004571383 (±0.051384017)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-294-294-294
Dimensions588588588
Spacing588588588
CellA=B=C: 492.156 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: The half-map A of the CPV2a-Fab 2C5 asymmetric complex

Fileemd_47694_half_map_1.map
AnnotationThe half-map A of the CPV2a-Fab 2C5 asymmetric complex
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: The half-map B of the CPV2a-Fab 2C5 asymmetric complex

Fileemd_47694_half_map_2.map
AnnotationThe half-map B of the CPV2a-Fab 2C5 asymmetric 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 2
    • Protein or peptide: Heavy chain antibody fragment
    • Protein or peptide: Light chain antibody fragment

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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 2

MacromoleculeName: Capsid protein 2 / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Canine parvovirus 2a
Molecular weightTheoretical: 61.602359 KDa
Recombinant expressionOrganism: Felis catus (domestic cat)
SequenceString: GVGISTGTFN NQTEFKFLEN GWVYITANSS RLVHLNMPES ENYRRVVVNN LDKTAVNGNM ALDDTHAEIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI ...String:
GVGISTGTFN NQTEFKFLEN GWVYITANSS RLVHLNMPES ENYRRVVVNN LDKTAVNGNM ALDDTHAEIV TPWSLVDANA WGVWFNPGD WQLIVNTMSE LHLVSFEQEI FNVVLKTVSE SATQPPTKVY NNDLTASLMV ALDSNNTMPF TPAAMRSETL G FYPWKPTI PTPWRYYFQW DRTLIPSHTG TSGTPTNIYH GTDPDDVQFY TIENSVPVHL LRTGDEFATG TFFFDCKPCR LT HTWQTNR ALGLPPFLNS LPQSEGGTNF GYIGVQQDKR RGVTQMGNTN YITEATIMRP AEVGYSAPYY SFEASTQGPF KTP IAAGRG GAQTDENQAA DGDPRYAFGR QHGQKTTTTG ETPERFTYIA HQDTGRYPEG DWIQNINFNL PVTDDNVLLP TDPI GGKTG INYTNIFNTY GPLTALNNVP PVYPNGQIWD KEFDTDLKPR LHVNAPFVCQ NNCPGQLFVK VAPNLTNQYD PDASA NMSR IVTYSDFWWK GKLVFKAKLR ASHTWNPIQQ MSINVDNQFN YVPSNIGGMK IVYEKSQLAP RKLY

UniProtKB: Capsid protein 2

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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: 13.629223 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
EVQLVESGGD LVKPAGSLRL SCVASGFTFS SYGMNWVRQA PGKGLQWVAG VNSGGFTGYA DAVKGRFTIS RDNAKNTVYL QMNSLTAED TAVYYCAKDR YYCTGDYCFN LIAFGYWGQG TLVTVSS

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Macromolecule #3: Light chain antibody fragment

MacromoleculeName: Light chain antibody fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Canis lupus familiaris (dog)
Molecular weightTheoretical: 11.312431 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
QSVLTQPTSV SGSLGQRVTI SCSGSTNNIG IVGASWYQQL PGKAPKLLVY SDGNRPSGVP DRFSGSNSGN SATLTITGLQ AEDEADYYC QSVDPTLGVV VFGGGTHLTV L

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 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
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 725715
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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