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- EMDB-1234: West Nile virus in complex with the Fab fragment of a neutralizin... -

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Basic information

Entry
Database: EMDB / ID: EMD-1234
TitleWest Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody.
Map datamap of West Nile Virus complexed with Fab fragment of neutralizing antibody E16
Sample
  • Sample: West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
  • Virus: West Nile virus
  • Protein or peptide: E16 Fab fragment
Biological speciesunidentified (others) / West Nile virus
Methodsingle particle reconstruction / cryo EM / Resolution: 14.5 Å
AuthorsKaufmann B / Nybakken GE / Chipman PR / Zhang W / Diamond MS / Fremont DH / Kuhn RJ / Rossmann MG
CitationJournal: Proc Natl Acad Sci U S A / Year: 2006
Title: West Nile virus in complex with the Fab fragment of a neutralizing monoclonal antibody.
Authors: Bärbel Kaufmann / Grant E Nybakken / Paul R Chipman / Wei Zhang / Michael S Diamond / Daved H Fremont / Richard J Kuhn / Michael G Rossmann /
Abstract: Flaviviruses, such as West Nile virus (WNV), are significant human pathogens. The humoral immune response plays an important role in the control of flavivirus infection and disease. The structure of ...Flaviviruses, such as West Nile virus (WNV), are significant human pathogens. The humoral immune response plays an important role in the control of flavivirus infection and disease. The structure of WNV complexed with the Fab fragment of the strongly neutralizing mAb E16 was determined to 14.5-Angstrom resolution with cryo-electron microscopy. E16, an antibody with therapeutic potential, binds to domain III of the WNV envelope glycoprotein. Because of steric hindrance, Fab E16 binds to only 120 of the 180 possible binding sites on the viral surface. Fitting of the previously determined x-ray structure of the Fab-domain III complex into the cryo-electron microscopy density required a change of the elbow angle between the variable and constant domains of the Fab. The structure suggests that the E16 antibody neutralizes WNV by blocking the initial rearrangement of the E glycoprotein before fusion with a cellular membrane.
History
DepositionJun 29, 2006-
Header (metadata) releaseJun 29, 2006-
Map releaseSep 5, 2006-
UpdateSep 25, 2013-
Current statusSep 25, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3589.788788697
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3589.788788697
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1234.gif

Downloads & links

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Map

FileDownload / File: emd_1234.map.gz / Format: CCP4 / Size: 101.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap of West Nile Virus complexed with Fab fragment of neutralizing antibody E16
Voxel sizeX=Y=Z: 2.7459 Å
Density
Contour LevelBy AUTHOR: 611.0 / Movie #1: 3589.7887887
Minimum - Maximum-1499.927734379999947 - 11314.149414060000709
Average (Standard dev.)703.748352049999994 (±1973.494140629999947)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-150-150-150
Dimensions301301301
Spacing301301301
CellA=B=C: 826.51587 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.74590033222592.74590033222592.7459003322259
M x/y/z301301301
origin x/y/z0.0000.0000.000
length x/y/z826.516826.516826.516
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS301301301
D min/max/mean-1499.92811314.149703.748

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Supplemental data

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Sample components

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Entire : West Nile virus NY99 complexed with Fab fragment of neutralizing ...

EntireName: West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
Components
  • Sample: West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
  • Virus: West Nile virus
  • Protein or peptide: E16 Fab fragment

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Supramolecule #1000: West Nile virus NY99 complexed with Fab fragment of neutralizing ...

SupramoleculeName: West Nile virus NY99 complexed with Fab fragment of neutralizing monoclonal antibody E16
type: sample / ID: 1000
Oligomeric state: T1 icosahedron with three E monomers and two Fab per asymmetric unit
Number unique components: 2

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Supramolecule #1: West Nile virus

SupramoleculeName: West Nile virus / type: virus / ID: 1 / Name.synonym: WNV / NCBI-ID: 11082 / Sci species name: West Nile virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: WNV
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Virus shellShell ID: 1 / Name: E glycoprotein / Diameter: 500 Å / T number (triangulation number): 1

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Macromolecule #1: E16 Fab fragment

MacromoleculeName: E16 Fab fragment / type: protein_or_peptide / ID: 1 / Number of copies: 120 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: unidentified (others)
Recombinant expressionOrganism: mammalian cell line (unknown)

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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

BufferpH: 8 / Details: 12 mM Tris-HCl, 120 mM NaCl, 1 mM EDTA
GridDetails: 400 mesh copper grid
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Guillotine-style plunge freezeing device
Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine ...Method: A small vial of ethane is placed inside a larger liquid nitrogen reservoir. The grid holding a few microliters of the sample is held in place at the bottom of a plunger by the means of fine tweezers. Once the ethane in the vial is completely frozen, it needs to be slightly melted. When the liquid ethane is ready, a piece of filter paper is then pressed against the sample to blot of excess buffer, sufficient to leave a thin layer on the grid. After a predetermined time, the filter paper is removed, and the plunger is allowed to drop into the liquid ethane. Once the grid enters the liquid ethane, the sample is rapidly frozen, and the grid is transferred under liquid nitrogen to a storage box immersed liquid nitrogen for later use in the microscope.

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/T
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 47190 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 3.88 µm / Nominal defocus min: 1.32 µm / Nominal magnification: 47000
Sample stageSpecimen holder: EUCENTRIC / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 98 K
Alignment procedureLegacy - Astigmatism: live FFT at 200K mag
Detailslow dose
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Number real images: 78 / Average electron dose: 22 e/Å2 / Details: Nikon SuperCoolScan 9K scanned images binned 2x2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Each particle
Final angle assignmentDetails: theta 69 to 90 degrees phi -31 to 31 degrees omega 0 to 360 degrees
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: PFTSEARCH, PO2R, P3DR
Details: final map includes data to 12.8 Ang resolution (fsc 0.3 cut-off); magnification of final map standardized to a map calculated from dengue virus model coordinates (PDB accession no 1THD)
Number images used: 3567
DetailsThe particles were selected interactively at the computer terminal.

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Atomic model buiding 1

Initial modelPDB ID:

1thd

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