- EMDB-6629: Near-atomic structure of Canine Parvovirus complexed with Fab E -
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Basic information
Entry
Database: EMDB / ID: EMD-6629
Title
Near-atomic structure of Canine Parvovirus complexed with Fab E
Map data
Reconstruction of CPV-FAB E complex
Sample
Sample: Canine Parvovirus complexed with Fab E
Virus: Canine parvovirus
Protein or peptide: Fab E
Keywords
parvovirus / single particle / canine parvovirus / fab / antibody / complex
Function / homology
Function and homology information
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
Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus Similarity search - Domain/homology
Journal: J Virol / Year: 2016 Title: Near-Atomic Resolution Structure of a Highly Neutralizing Fab Bound to Canine Parvovirus. Authors: Lindsey J Organtini / Hyunwook Lee / Sho Iketani / Kai Huang / Robert E Ashley / Alexander M Makhov / James F Conway / Colin R Parrish / Susan Hafenstein / Abstract: Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was ...Canine parvovirus (CPV) is a highly contagious pathogen that causes severe disease in dogs and wildlife. Previously, a panel of neutralizing monoclonal antibodies (MAb) raised against CPV was characterized. An antibody fragment (Fab) of MAb E was found to neutralize the virus at low molar ratios. Using recent advances in cryo-electron microscopy (cryo-EM), we determined the structure of CPV in complex with Fab E to 4.1 Å resolution, which allowed de novo building of the Fab structure. The footprint identified was significantly different from the footprint obtained previously from models fitted into lower-resolution maps. Using single-chain variable fragments, we tested antibody residues that control capsid binding. The near-atomic structure also revealed that Fab binding had caused capsid destabilization in regions containing key residues conferring receptor binding and tropism, which suggests a mechanism for efficient virus neutralization by antibody. Furthermore, a general technical approach to solving the structures of small molecules is demonstrated, as binding the Fab to the capsid allowed us to determine the 50-kDa Fab structure by cryo-EM. IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced ...IMPORTANCE: Using cryo-electron microscopy and new direct electron detector technology, we have solved the 4 Å resolution structure of a Fab molecule bound to a picornavirus capsid. The Fab induced conformational changes in regions of the virus capsid that control receptor binding. The antibody footprint is markedly different from the previous one identified by using a 12 Å structure. This work emphasizes the need for a high-resolution structure to guide mutational analysis and cautions against relying on older low-resolution structures even though they were interpreted with the best methodology available at the time.
History
Deposition
Mar 18, 2016
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Header (metadata) release
Mar 30, 2016
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Map release
Mar 30, 2016
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Update
Nov 2, 2016
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Current status
Nov 2, 2016
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
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