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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
TitleStructure of MA28-7 neutralizing antibody Fab fragment from electron cryo-microscopy of enterovirus 71 complexed with a Fab fragment
Components
  • MA28-7 neutralizing antibody heavy chain
  • MA28-7 neutralizing antibody light chain
KeywordsIMMUNE SYSTEM / EV71 / enterovirus / HFMD / strain-specific eptitope / VP1-145
Biological speciesMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 23.4 Å
AuthorsLee, H. / Cifuente, J.O. / Ashley, R.E. / Conway, J.F. / Makhov, A.M. / Tano, Y. / Shimizu, H. / Nishimura, Y. / Hafenstein, S.
CitationJournal: J Virol / Year: 2013
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
DepositionMay 21, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Apr 9, 2014Group: Source and taxonomy
Revision 1.3Jul 18, 2018Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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Assembly

Deposited unit
L: MA28-7 neutralizing antibody light chain
H: MA28-7 neutralizing antibody heavy chain


Theoretical massNumber of molelcules
Total (without water)46,6112
Polymers46,6112
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Antibody MA28-7 neutralizing antibody light chain


Mass: 23261.770 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MA28-7 neutralizing antibody heavy chain


Mass: 23349.105 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
Type: VIRUS
Molecular weightValue: 8.05 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: STRAIN / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.5 / Details: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: glow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationInstrument: 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
MicroscopyModel: FEI TECNAI F20 / Date: Feb 2, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy / 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 holderSpecimen holder model: GATAN LIQUID NITROGEN / Temperature: 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNum. digital images: 45
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

EM software
IDNameVersionCategory
1UCSF Chimeramodel fitting
2EMAN23D reconstruction
CTF correctionDetails: Each
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionMethod: 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 buildingProtocol: 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
IDPDB-IDPdb chain-ID 3D fitting-ID
13GK8H1
23GK8L1
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms3283 0 0 0 3283

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