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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-23658 | |||||||||
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Title | Canine parvovirus and Fab14 asymmetric reconstruction | |||||||||
![]() | Canine parvovirus and Fab14 asymmetric reconstruction | |||||||||
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Function / homology | ![]() permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner 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 | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.4 Å | |||||||||
![]() | Goteschius DJ / Hartmann SR / Hafenstein SL | |||||||||
Funding support | ![]()
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![]() | ![]() Title: High-resolution asymmetric structure of a Fab-virus complex reveals overlap with the receptor binding site. Authors: Daniel J Goetschius / Samantha R Hartmann / Lindsey J Organtini / Heather Callaway / Kai Huang / Carol M Bator / Robert E Ashley / Alexander M Makhov / James F Conway / Colin R Parrish / Susan L Hafenstein / ![]() Abstract: Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids ...Canine parvovirus is an important pathogen causing severe diseases in dogs, including acute hemorrhagic enteritis, myocarditis, and cerebellar disease. Overlap on the surface of parvovirus capsids between the antigenic epitope and the receptor binding site has contributed to cross-species transmission, giving rise to closely related variants. It has been shown that Mab 14 strongly binds and neutralizes canine but not feline parvovirus, suggesting this antigenic site also controls species-specific receptor binding. To visualize the conformational epitope at high resolution, we solved the cryogenic electron microscopy (cryo-EM) structure of the Fab-virus complex. We also created custom software, Icosahedral Subparticle Extraction and Correlated Classification, to solve a Fab-virus complex with only a few Fab bound per capsid and visualize local structures of the Fab-bound and -unbound antigenic sites extracted from the same complex map. Our results identified the antigenic epitope that had significant overlap with the receptor binding site, and the structures revealed that binding of Fab induced conformational changes to the virus. We were also able to assign the order and position of attached Fabs to allow assessment of complementarity between the Fabs bound to different positions. This approach therefore provides a method for using cryo-EM to investigate complementarity of antibody binding. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 326.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 16.4 KB 16.4 KB | Display Display | ![]() |
Images | ![]() | 106.5 KB | ||
Others | ![]() ![]() | 296.1 MB 296.2 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7m3nMC ![]() 7m3lC ![]() 7m3mC ![]() 7m3oC M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Canine parvovirus and Fab14 asymmetric reconstruction | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Half map: Half-map 1
File | emd_23658_half_map_1.map | ||||||||||||
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Annotation | Half-map 1 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half-map 2
File | emd_23658_half_map_2.map | ||||||||||||
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Annotation | Half-map 2 | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Canine parvovirus and FAB
Entire | Name: Canine parvovirus and FAB |
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Components |
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-Supramolecule #1: Canine parvovirus and FAB
Supramolecule | Name: Canine parvovirus and FAB / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: FAB
Supramolecule | Name: FAB / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #3: Canine parvovirus
Supramolecule | Name: Canine parvovirus / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: CPV Fab14 light chain
Macromolecule | Name: CPV Fab14 light chain / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 11.981362 KDa |
Sequence | String: DIVMTQSHKF MSTSVGDRVS ITCKASQDVN TALAWYQQIP GQSPKLLIYS ASNRYTGVPD RFTASGSGTD FTFTISSVQA EDLALYYCQ QHYTTPWTFG GGTKLEIKR |
-Macromolecule #2: CPV Fab14 heavy chain
Macromolecule | Name: CPV Fab14 heavy chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() ![]() |
Molecular weight | Theoretical: 13.10453 KDa |
Sequence | String: AVHLQGTELV KPGASAGVKL SCKASGYTFT NYDMNWVRQR PEQGLEWIGW IFPGDGSTRY NEKFKGKATL TTDKSSSTAY QLNRLTSED SAVYFCARRG SHGSYSFAYW GQGTLVTVSG |
-Macromolecule #3: Capsid protein 2
Macromolecule | Name: Capsid protein 2 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 64.705559 KDa |
Sequence | String: MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVE ITANSSRLVH LNMPESENYR RVVVNNMDK TAVNGNMALD DIHAQIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND ...String: MSDGAVQPDG GQPAVRNERA TGSGNGSGGG GGGGSGGVGI STGTFNNQTE FKFLENGWVE ITANSSRLVH LNMPESENYR RVVVNNMDK TAVNGNMALD DIHAQIVTPW SLVDANAWGV WFNPGDWQLI VNTMSELHLV SFEQEIFNVV LKTVSESATQ P PTKVYNND LTASLMVALD SNNTMPFTPA AMRSETLGFY PWKPTIPTPW RYYFQWDRTL IPSHTGTSGT PTNIYHGTDP DD VQFYTIE NSVPVHLLRT GDEFATGTFF FDCKPCRLTH TWQTNRALGL PPFLNSLPQS EGATNFGDIG VQQDKRRGVT QMG NTNYIT EATIMRPAEV GYSAPYYSFE ASTQGPFKTP IAAGRGGAQT DENQAADGNP RYAFGRQHGQ KTTTTGETPE RFTY IAHQD TGRYPEGDWI QNINFNLPVT NDNVLLPTDP IGGKTGINYT NIFNTYGPLT ALNNVPPVYP NGQIWDKEFD TDLKP RLHV NAPFVCQNNC PGQLFVKVAP NLTNEYDPDA SANMSRIVTY SDFWWKGKLV FKAKLRASHT WNPIQQMSIN VDNQFN YVP SNIGGMKIVY EKSQLAPRKL Y |
-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: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF Details: Asymmetric reconstruction, particle number is 162,627*10.2 orientations per particle Number images used: 162627 |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: OTHER |