+Open data
-Basic information
Entry | Database: PDB / ID: 3jcx | ||||||
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Title | Canine Parvovirus complexed with Fab E | ||||||
Components |
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Keywords | VIRUS/IMMUNE SYSTEM / parvovirus / antibody / VIRUS-IMMUNE SYSTEM 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 | ||||||
Biological species | Canine parvovirus Rattus norvegicus (Norway rat) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
Authors | Organtini, L.J. / Iketani, S. / Huang, K. / Ashley, R.E. / Makhov, A.M. / Conway, J.F. / Parrish, C.R. / Hafenstein, S. | ||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3jcx.cif.gz | 148.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3jcx.ent.gz | 118.7 KB | Display | PDB format |
PDBx/mmJSON format | 3jcx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3jcx_validation.pdf.gz | 896.9 KB | Display | wwPDB validaton report |
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Full document | 3jcx_full_validation.pdf.gz | 933.4 KB | Display | |
Data in XML | 3jcx_validation.xml.gz | 33.3 KB | Display | |
Data in CIF | 3jcx_validation.cif.gz | 47.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jc/3jcx ftp://data.pdbj.org/pub/pdb/validation_reports/jc/3jcx | HTTPS FTP |
-Related structure data
Related structure data | 6629MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 64783.629 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canine parvovirus / References: UniProt: B2ZG07 |
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#2: Antibody | Mass: 12739.242 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Strain: B5A8 |
#3: Antibody | Mass: 11745.118 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / Strain: B5A8 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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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: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: Quantifoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Details: Plunged into liquid ethane (FEI VITROBOT MARK II). |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 4000 nm / Nominal defocus min: 1500 nm |
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 |
-Processing
EM software | Name: RELION / Category: 3D reconstruction | ||||||||||||
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Symmetry | Point symmetry: I (icosahedral) | ||||||||||||
3D reconstruction | Method: Single Particle / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 47563 / Nominal pixel size: 1.37 Å / Actual pixel size: 1.37 Å / Symmetry type: POINT | ||||||||||||
Refinement step | Cycle: LAST
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