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Yorodumi- PDB-6nn3: Structure of parvovirus B19 decorated with Fab molecules from a h... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nn3 | |||||||||
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Title | Structure of parvovirus B19 decorated with Fab molecules from a human antibody | |||||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / B19 / VP2 / antibody / epitope / VIRUS LIKE PARTICLE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Human parvovirus B19 Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.22 Å | |||||||||
Authors | Rossmann, M.G. / Sun, Y. / Klose, T. / Liu, Y. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J Virol / Year: 2019 Title: Structure of Parvovirus B19 Decorated by Fabs from a Human Antibody. Authors: Yingyuan Sun / Thomas Klose / Yue Liu / Susanne Modrow / Michael G Rossmann / Abstract: Parvovirus B19, one of the most common human pathogens, is a small DNA virus that belongs to the As a result of previous infections, antibodies to B19 are present in most adults. B19 has a strong ...Parvovirus B19, one of the most common human pathogens, is a small DNA virus that belongs to the As a result of previous infections, antibodies to B19 are present in most adults. B19 has a strong tropism to erythroid progenitor cells and is able to cause a series of medical conditions, including fifth disease, arthritis, myocarditis, hydrops fetalis, and aplastic crisis. No approved vaccine is currently available for B19, and there is a lack of structural characterization of any B19 epitopes. Here we present the first cryo-electron microscopy (cryo-EM) structure of a B19 virus-like particle (VLP) complexed with the antigen-binding fragment (Fab) of a human neutralizing antibody, 860-55D. A model was built into the 3.2-Å-resolution map, and the antigenic residues on the surface of the B19 capsid were identified. Antibody 860-55D bridges the capsid of B19 by binding to a quaternary structure epitope formed by residues from three neighboring VP2 capsid proteins. Parvovirus B19 is a common human pathogen and a particular threat to children, pregnant women, and patients with sickle cell disease or AIDS. Currently, neutralizing antibody is the most efficient treatment for acute B19 infections. Research on the antigenic properties of B19 will guide the usage of these antibodies and facilitate vaccine development. We have determined and report here the high-resolution structure of B19 virus-like particles (VLPs) complexed with the Fab of a human neutralizing antibody. The structure shows a quaternary structure epitope formed by three VP2 proteins and provides details on host recognition of human B19 virus. | |||||||||
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 | 6nn3.cif.gz | 141.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nn3.ent.gz | 114.4 KB | Display | PDB format |
PDBx/mmJSON format | 6nn3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nn/6nn3 ftp://data.pdbj.org/pub/pdb/validation_reports/nn/6nn3 | HTTPS FTP |
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-Related structure data
Related structure data | 9110MC 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: 60946.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human parvovirus B19 / Gene: VP1 / Production host: unidentified baculovirus / References: UniProt: Q75U93 |
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#2: Antibody | Mass: 13095.569 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
#3: Antibody | Mass: 10895.869 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
-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 | Name: complex of human parvovirus B19 major capsid protein VP2 with Fab molecules from a human neutralizing antibody Type: COMPLEX / Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Value: 5.4 MDa / Experimental value: NO |
Source (natural) | Organism: Human parvovirus B19 |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: B19 VLPs were incubated with purified Fab molecules overnight at 4 degrees. |
Specimen support | Grid material: COPPER |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 22500 X / Calibrated magnification: 22500 X / Nominal defocus max: 3000 nm / Nominal defocus min: 1000 nm / Calibrated defocus min: 1000 nm / Calibrated defocus max: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature (max): 100 K / Temperature (min): 70 K |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 38 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1759 |
Image scans | Width: 3838 / Height: 3710 / Movie frames/image: 40 / Used frames/image: 1-40 |
-Processing
Software | Name: PHENIX / Version: 1.14_3260: / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
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EM software |
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Image processing | Details: Motion corrected | ||||||||||||||||||||||||||||||||||||||||
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 9120 | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Method: SINGLE PARTICLESingle particle analysis / Resolution: 3.22 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 7395 / Algorithm: BACK PROJECTION / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL |