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- PDB-3j3z: Structure of MA28-7 neutralizing antibody Fab fragment from elect... -

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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
Specimen sourceMus musculus (house mouse)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / 23.4 Å resolution
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
Validation Report
SummaryFull reportAbout validation report
DateDeposition: May 21, 2013 / Release: Aug 28, 2013
RevisionDateData content typeGroupCategoryItemProviderType
1.0Aug 28, 2013Structure modelrepositoryInitial release
1.1Nov 6, 2013Structure modelDatabase references
1.2Apr 9, 2014Structure modelSource and taxonomy
1.3Jul 18, 2018Structure modelData collectionem_software_em_software.image_processing_id

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  • Imaged by UCSF Chimera
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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
Polyers46,6112
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein/peptide MA28-7 neutralizing antibody light chain


Mass: 23261.770 Da / Num. of mol.: 1 / Fragment: Fab / Source: (natural) Mus musculus (house mouse)
#2: Protein/peptide MA28-7 neutralizing antibody heavy chain


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

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 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 / Virus host category: VERTEBRATES / Virus isolate: STRAIN / Virus type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionDetails: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2 / pH: 7.5
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
MicroscopyMicroscope model: 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 / Calibrated magnification: 48425 / 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 kelvins / Tilt angle max: 0 deg. / Tilt angle min: 0 deg.
Image recordingElectron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM
Image scansNumber digital images: 45
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m 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
3D reconstructionMethod: Cross correlation coefficient / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Number of particles: 27026 / Nominal pixel size: 1.23 / Actual pixel size: 1.23
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)
Number of class averages: 2300 / Symmetry type: POINT
Atomic model buildingDetails: REFINEMENT PROTOCOL--rigid body DETAILS--The Fab structure was fitted manually, then refined in Chimera.
Ref protocol: RIGID BODY FIT / Ref space: REAL / Target criteria: correlation coefficient
Atomic model building
IDPDB-IDPdb chain ID 3D fitting ID
13GK8H1
23GK8L1
Number of atoms included #LASTProtein: 3283 / Nucleic acid: 0 / Ligand: 0 / Solvent: 0 / Total: 3283

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