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- PDB-3j3z: Structure of MA28-7 neutralizing antibody Fab fragment from elect... -
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Basic information
Entry | Database: PDB / ID: 3j3z | ||||||
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Title | Structure of MA28-7 neutralizing antibody Fab fragment from electron cryo-microscopy of enterovirus 71 complexed with a Fab fragment | ||||||
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![]() | IMMUNE SYSTEM / EV71 / enterovirus / HFMD / strain-specific eptitope / VP1-145 | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 23.4 Å | ||||||
![]() | Lee, H. / Cifuente, J.O. / Ashley, R.E. / Conway, J.F. / Makhov, A.M. / Tano, Y. / Shimizu, H. / Nishimura, Y. / Hafenstein, S. | ||||||
![]() | ![]() Title: A strain-specific epitope of enterovirus 71 identified by cryo-electron microscopy of the complex with fab from neutralizing antibody. Authors: Hyunwook Lee / Javier O Cifuente / Robert E Ashley / James F Conway / Alexander M Makhov / Yoshio Tano / Hiroyuki Shimizu / Yorihiro Nishimura / Susan Hafenstein / ![]() Abstract: Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 ...Enterovirus 71 (EV71) is a picornavirus that causes outbreaks of hand, foot, and mouth disease (HFMD), primarily in the Asia-Pacific area. Unlike coxsackievirus A16, which also causes HFMD, EV71 induces severe neuropathology leading to high fatalities, especially among children under the age of 6 years. Currently, no established vaccines or treatments are available against EV71 infection. The monoclonal antibody MA28-7 neutralizes only specific strains of EV71 that have a conserved glycine at amino acid VP1-145, a surface-exposed residue that maps to the 5-fold vertex and that has been implicated in receptor binding. The cryo-electron microscopy structure of a complex between EV71 and the Fab fragment of MA28-7 shows that only one Fab fragment occupies each 5-fold vertex. A positively charged patch, which has also been implicated in receptor binding, lies within the Fab footprint. We identify the strain-specific epitope of EV71 and discuss the possible neutralization mechanisms of the antibody. | ||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 88.8 KB | Display | ![]() |
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PDB format | ![]() | 70.5 KB | Display | ![]() |
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-Validation report
Summary document | ![]() | 696.8 KB | Display | ![]() |
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Full document | ![]() | 707.6 KB | Display | |
Data in XML | ![]() | 22.2 KB | Display | |
Data in CIF | ![]() | 30.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5673MC 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
Deposited unit | ![]()
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Components
#1: Antibody | Mass: 23261.770 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Antibody | Mass: 23349.105 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody Type: VIRUS |
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Molecular weight | Value: 8.05 MDa / Experimental value: NO |
Details of virus | Empty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION |
Natural host | Organism: Homo sapiens |
Buffer solution | pH: 7.5 / Details: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: glow-discharged holey carbon Quantifoil electron microscopy grids |
Vitrification | Instrument: FEI VITROBOT MARK III / Cryogen name: OTHER / Temp: 76 K / Humidity: 95 % Details: Plunged into ethane-propane mixture (FEI VITROBOT MARK III) |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Feb 2, 2011 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Calibrated magnification: 48425 X / Nominal defocus max: 6120 nm / Nominal defocus min: 1900 nm / Cs: 2 mm / Camera length: 0 mm |
Specimen holder | Specimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 ° |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 45 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
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Processing
EM software |
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CTF correction | Details: Each | ||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||
3D reconstruction | Method: Cross correlation coefficient / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Num. of particles: 27026 / Nominal pixel size: 1.23 Å / Actual pixel size: 1.23 Å Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations. (Single particle details: Selected particles were low-pass filtered at 10 Angstrom. Asymmetric ...Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations. (Single particle details: Selected particles were low-pass filtered at 10 Angstrom. Asymmetric reconstruction was performed with the breaksym option in EMAN2.) (Single particle--Applied symmetry: C1) Num. of class averages: 2300 / Symmetry type: POINT | ||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: correlation coefficient Details: REFINEMENT PROTOCOL--rigid body DETAILS--The Fab structure was fitted manually, then refined in Chimera. | ||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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