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- EMDB-5673: Electron cryo-microscopy of enterovirus 71 complexed with a Fab f... -

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Basic information

Entry
Database: EMDB / ID: EMD-5673
TitleElectron cryo-microscopy of enterovirus 71 complexed with a Fab fragment
Map dataAsymmetric reconstruction of ev71-Fab complex
Sample
  • Sample: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
  • Virus: Human enterovirus 71
  • Protein or peptide: MA28-7 neutralizing antibody Fab fragment
KeywordsEV71 / enterovirus / HFMD / neutralizing antibody / Fab / cryoEM / strain-specific eptitope / VP1-145
Biological speciesMus musculus (house mouse) / Human enterovirus 71
Methodsingle particle reconstruction / cryo EM / Resolution: 23.4 Å
AuthorsLee H / Cifuente JO / Ashley RE / Conway JF / Makhov AM / 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, 2013-
Header (metadata) releaseJun 26, 2013-
Map releaseAug 28, 2013-
UpdateNov 6, 2013-
Current statusNov 6, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-3j3z
  • Surface level: 1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3j3z
  • Imaged by Jmol
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Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5673.map.gz / Format: CCP4 / Size: 412 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationAsymmetric reconstruction of ev71-Fab complex
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-8.519919399999999 - 13.191069600000001
Average (Standard dev.)0.15144682 (±1.46808076)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-240-240-240
Dimensions480480480
Spacing480480480
CellA=B=C: 590.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z480480480
origin x/y/z0.0000.0000.000
length x/y/z590.400590.400590.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-240-240-240
NC/NR/NS480480480
D min/max/mean-8.52013.1910.151

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Supplemental data

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Sample components

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Entire : Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing...

EntireName: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
Components
  • Sample: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
  • Virus: Human enterovirus 71
  • Protein or peptide: MA28-7 neutralizing antibody Fab fragment

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Supramolecule #1000: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing...

SupramoleculeName: Enterovirus 71 complexed with Fab Fragment of MA28-7 neutralizing antibody
type: sample / ID: 1000 / Number unique components: 2
Molecular weightTheoretical: 8.05 MDa

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Supramolecule #1: Human enterovirus 71

SupramoleculeName: Human enterovirus 71 / type: virus / ID: 1 / Name.synonym: EV71 / Details: Fab fragment is bound on the virus surface / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Sci species strain: 1095/Shiga / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No / Syn species name: EV71
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 8 MDa
Virus shellShell ID: 1 / Name: VP1-4 / Diameter: 300 Å / T number (triangulation number): 1

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Macromolecule #1: MA28-7 neutralizing antibody Fab fragment

MacromoleculeName: MA28-7 neutralizing antibody Fab fragment / type: protein_or_peptide / ID: 1 / Recombinant expression: No / Database: NCBI
Source (natural)Organism: Mus musculus (house mouse) / Strain: BALB/c / synonym: mouse / Cell: hybridomas fused with myeloma cells

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1.0 mg/mL
BufferpH: 7.5 / Details: 10 mM Tris, 200 mM NaCl, 50 mM MgCl2
GridDetails: glow-discharged holey carbon Quantifoil electron microscopy grids
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 95 % / Chamber temperature: 76 K / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 48425 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2 mm / Nominal defocus max: 6.12 µm / Nominal defocus min: 1.9 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 95 K
DateFeb 2, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Number real images: 45 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each image
Final two d classificationNumber classes: 2300
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 23.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2
Details: The breaksym option in EMAN2 was used to search for the icosahedrally-related orientations.
Number images used: 27026
DetailsSelected particles were low-pass filtered at 10 Angstrom. Asymmetric reconstruction was performed with breaksym option in EMAN2.

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Atomic model buiding 1

Initial modelPDB ID:

Chain - #0 - Chain ID: H / Chain - #1 - Chain ID: L
SoftwareName: Chimera
DetailsThe Fab structure was fitted manually, then refined in Chimera.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: correlation coefficient
Output model

PDB-3j3z:
Structure of MA28-7 neutralizing antibody Fab fragment from electron cryo-microscopy of enterovirus 71 complexed with a Fab fragment

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