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Open data
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Basic information
Entry | Database: PDB / ID: 3jcx | ||||||
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Title | Canine Parvovirus complexed with Fab E | ||||||
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![]() | VIRUS/IMMUNE SYSTEM / ![]() ![]() | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Organtini, L.J. / Iketani, S. / Huang, K. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Parrish, C.R. / Hafenstein, S. | ||||||
![]() | ![]() 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. | ||||||
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148.8 KB | Display | ![]() |
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PDB format | ![]() | 118.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6629MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
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Symmetry | Point symmetry: (Schoenflies symbol![]() ![]() |
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Components
#1: Protein | ![]() Mass: 64783.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 12739.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
#3: Antibody | Mass: 11745.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: ![]() |
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Sample preparation
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Details of virus | Empty: YES / Enveloped: NO / Host category: CANINES / Isolate: SPECIES / Type: VIRION | |||||||||||||||||||||||||
Natural host | Organism: Canis lupus | |||||||||||||||||||||||||
Buffer solution | Name: PBS / pH: 7.4 / Details: PBS | |||||||||||||||||||||||||
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied![]() ![]() | |||||||||||||||||||||||||
Specimen support | Details: Quantifoil | |||||||||||||||||||||||||
Vitrification![]() | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK II). |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Dec 20, 2014 |
Electron gun | Electron source![]() ![]() |
Electron lens | Mode: BRIGHT FIELD![]() |
Specimen holder | Specimen holder model: SIDE ENTRY, EUCENTRIC |
Image recording | Electron dose: 30 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
Image scans | Num. digital images: 1424 |
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Processing
EM software | Name: RELION / Category: 3D reconstruction![]() | ||||||||||||
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Symmetry | Point symmetry![]() ![]() | ||||||||||||
3D reconstruction![]() | Method: Single Particle![]() | ||||||||||||
Refinement step | Cycle: LAST
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