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- EMDB-5671: Cross-Neutralizing Human Anti-Poliovirus Antibodies Bind the Reco... -

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Basic information

Entry
Database: EMDB / ID: EMD-5671
TitleCross-Neutralizing Human Anti-Poliovirus Antibodies Bind the Recognition Site for Cellular Receptor
Map dataCryo-EM reconstruction of type 2 polio virus with A12 Fab attached
Sample
  • Sample: Fab Fragment of A12 antibody bound to Type 2 poliovirus
  • Virus: Human poliovirus 2
KeywordsPolio / Type 2 Polio / A12
Biological speciesHuman poliovirus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 20.0 Å
AuthorsChen Z / Fischer ER / Kouiavskaia D / Hansen BT / Ludtke SJ / Bidzhieva B / Makiya M / Purcell RH / Chumakov K
CitationJournal: Proc Natl Acad Sci U S A / Year: 2013
Title: Cross-neutralizing human anti-poliovirus antibodies bind the recognition site for cellular receptor.
Authors: Zhaochun Chen / Elizabeth R Fischer / Diana Kouiavskaia / Bryan T Hansen / Steven J Ludtke / Bella Bidzhieva / Michelle Makiya / Liane Agulto / Robert H Purcell / Konstantin Chumakov /
Abstract: Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of ...Most structural information about poliovirus interaction with neutralizing antibodies was obtained in the 1980s in studies of mouse monoclonal antibodies. Recently we have isolated a number of human/chimpanzee anti-poliovirus antibodies and demonstrated that one of them, MAb A12, could neutralize polioviruses of both serotypes 1 and 2. This communication presents data on isolation of an additional cross-neutralizing antibody (F12) and identification of a previously unknown epitope on the surface of poliovirus virions. Epitope mapping was performed by sequencing of antibody-resistant mutants and by cryo-EM of complexes of virions with Fab fragments. The results have demonstrated that both cross-neutralizing antibodies bind the site located at the bottom of the canyon surrounding the fivefold axis of symmetry that was previously shown to interact with cellular poliovirus receptor CD155. However, the same antibody binds to serotypes 1 and 2 through different specific interactions. It was also shown to interact with type 3 poliovirus, albeit with about 10-fold lower affinity, insufficient for effective neutralization. Antibody interaction with the binding site of the cellular receptor may explain its broad reactivity and suggest that further screening or antibody engineering could lead to a universal antibody capable of neutralizing all three serotypes of poliovirus.
History
DepositionMay 10, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseDec 11, 2013-
UpdateDec 18, 2013-
Current statusDec 18, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.7
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.7
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5671.map.gz / Format: CCP4 / Size: 50.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM reconstruction of type 2 polio virus with A12 Fab attached
Voxel sizeX=Y=Z: 1.8 Å
Density
Contour LevelBy AUTHOR: 0.7 / Movie #1: 0.7
Minimum - Maximum0.0 - 2.1542964
Average (Standard dev.)0.25201949 (±0.45818526)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin424141
Dimensions237239239
Spacing237239239
CellA: 430.19998 Å / B: 426.59998 Å / C: 430.19998 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.81.81.8
M x/y/z239237239
origin x/y/z0.0000.0000.000
length x/y/z430.200426.600430.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS414241
NC/NR/NS239237239
D min/max/mean0.0002.1540.252

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Supplemental data

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Sample components

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Entire : Fab Fragment of A12 antibody bound to Type 2 poliovirus

EntireName: Fab Fragment of A12 antibody bound to Type 2 poliovirus
Components
  • Sample: Fab Fragment of A12 antibody bound to Type 2 poliovirus
  • Virus: Human poliovirus 2

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Supramolecule #1000: Fab Fragment of A12 antibody bound to Type 2 poliovirus

SupramoleculeName: Fab Fragment of A12 antibody bound to Type 2 poliovirus
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Human poliovirus 2

SupramoleculeName: Human poliovirus 2 / type: virus / ID: 1 / NCBI-ID: 12083 / Sci species name: Human poliovirus 2 / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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 mg/mL
GridDetails: 4 uL aliquots of sample were applied to freshly glow-discharged 200 mesh r2/2 Quantifoil copper grids suspended by forceps in the FEI Mark IV Vitrobot.
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 65 K / Instrument: FEI VITROBOT MARK IV
Method: Specimens were vitrified, after blotting for 2 seconds with a blot force of 5 at 80% relative humidity, by plunge freezing into liquid ethane.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 80173 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 47000
Sample stageSpecimen holder: Liquid Nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 64 K / Max: 66 K / Average: 65 K
DateMar 3, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC CCD / Digitization - Sampling interval: 2 µm / Number real images: 150 / Average electron dose: 15 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final two d classificationNumber classes: 10
Final reconstructionResolution.type: BY AUTHOR / Resolution: 20.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 1500
DetailsParticles with a defocus range of 1-5 um were boxed with EMAN2, and then processed using the standard single particle reconstruction procedure with full CTF correction.

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Atomic model buiding 1

Initial modelPDB ID:

Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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