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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | CPV Total-Fab Polyclonal A Site Fab | |||||||||
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![]() | CPV / polyclonal Fab / A site / vaccination / VIRUS / VIRUS-IMMUNE SYSTEM complex | |||||||||
Function / homology | ![]() 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 / host cell / clathrin-dependent endocytosis of virus by host cell / entry receptor-mediated virion attachment to host cell / host cell nucleus ...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 / 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 | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
![]() | Hartmann SR / Hafenstein SL / Charnesky AJ | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 27.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 20.3 KB 20.3 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 9.1 KB | Display | ![]() |
Images | ![]() | 208.3 KB | ||
Filedesc metadata | ![]() | 5.7 KB | ||
Others | ![]() ![]() ![]() ![]() | 777.2 MB 398.3 MB 23 MB 23 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7utsMC ![]() 7utpC ![]() 7utrC ![]() 7utuC ![]() 7utvC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: #2
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-Additional map: #1
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-Half map: #2
File | emd_26788_half_map_1.map | ||||||||||||
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-Half map: #1
File | emd_26788_half_map_2.map | ||||||||||||
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Sample components
-Entire : Canine parvovirus in complex with antibody fragment
Entire | Name: Canine parvovirus in complex with antibody fragment |
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Components |
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-Supramolecule #1: Canine parvovirus in complex with antibody fragment
Supramolecule | Name: Canine parvovirus in complex with antibody fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Macromolecule #1: Capsid protein VP1
Macromolecule | Name: Capsid protein VP1 / type: protein_or_peptide / ID: 1 / Number of copies: 8 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 61.562367 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: 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 |
-Macromolecule #2: Light chain antibody fragment
Macromolecule | Name: Light chain antibody fragment / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 7.93277 KDa |
Sequence | 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) ...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) |
-Macromolecule #3: Heavy chain antibody fragment
Macromolecule | Name: Heavy chain antibody fragment / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 9.379553 KDa |
Sequence | 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) ...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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination 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 |