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- EMDB-3755: Cryo-EM map of Tick-borne encephalitis virus complexed with Fab f... -

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Basic information

Entry
Database: EMDB / ID: EMD-3755
TitleCryo-EM map of Tick-borne encephalitis virus complexed with Fab fragment of neutralizing antibody 19/1786 at pH 5.8
Map data
Sample
  • Virus: Tick-borne encephalitis virus (strain HYPR)
Biological speciesTick-borne encephalitis virus (strain HYPR)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.2 Å
AuthorsFuzik T / Plevka P
CitationJournal: Nat Commun / Year: 2018
Title: Structure of tick-borne encephalitis virus and its neutralization by a monoclonal antibody.
Authors: Tibor Füzik / Petra Formanová / Daniel Růžek / Kentaro Yoshii / Matthias Niedrig / Pavel Plevka /
Abstract: Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. ...Tick-borne encephalitis virus (TBEV) causes 13,000 cases of human meningitis and encephalitis annually. However, the structure of the TBEV virion and its interactions with antibodies are unknown. Here, we present cryo-EM structures of the native TBEV virion and its complex with Fab fragments of neutralizing antibody 19/1786. Flavivirus genome delivery depends on membrane fusion that is triggered at low pH. The virion structure indicates that the repulsive interactions of histidine side chains, which become protonated at low pH, may contribute to the disruption of heterotetramers of the TBEV envelope and membrane proteins and induce detachment of the envelope protein ectodomains from the virus membrane. The Fab fragments bind to 120 out of the 180 envelope glycoproteins of the TBEV virion. Unlike most of the previously studied flavivirus-neutralizing antibodies, the Fab fragments do not lock the E-proteins in the native-like arrangement, but interfere with the process of virus-induced membrane fusion.
History
DepositionJun 7, 2017-
Header (metadata) releaseJul 12, 2017-
Map releaseFeb 7, 2018-
UpdateApr 18, 2018-
Current statusApr 18, 2018Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3755.png

Downloads & links

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Map

FileDownload / File: emd_3755.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesY (Sec.)X (Row.)Z (Col.)
3 Å/pix.
x 256 pix.
= 768. Å		3 Å/pix.
x 256 pix.
= 768. Å		3 Å/pix.
x 256 pix.
= 768. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.3 / Movie #1: 1.3
Minimum - Maximum-4.092805 - 6.3635893
Average (Standard dev.)-0.000000002590555 (±1.)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZXY
Origin-128-128-128
Dimensions256256256
Spacing256256256
CellA=B=C: 768.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z333
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z768.000768.000768.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-128-128-128
NX/NY/NZ256256256
MAP C/R/S312
start NC/NR/NS-128-128-128
NC/NR/NS256256256
D min/max/mean-4.0936.364-0.000

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Supplemental data

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Sample components

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Entire : Tick-borne encephalitis virus (strain HYPR)

EntireName: Tick-borne encephalitis virus (strain HYPR)
Components
  • Virus: Tick-borne encephalitis virus (strain HYPR)

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Supramolecule #1: Tick-borne encephalitis virus (strain HYPR)

SupramoleculeName: Tick-borne encephalitis virus (strain HYPR) / type: virus / ID: 1 / Parent: 0 / Macromolecule list: #1-#4 / NCBI-ID: 70733
Sci species name: Tick-borne encephalitis virus (strain HYPR)
Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No
Virus shellShell ID: 1 / Name: Mature particle / Diameter: 500.0 Å / T number (triangulation number): 3

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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: 5.8
Component:
ConcentrationFormulaName
20.0 mMTrisTris
120.0 mMNaClsodium cloride
1.0 mMEDTAEthylenediaminetetraacetic acid
10.0 mMMES2-(N-morpholino)ethanesulfonic acid
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: NITROGEN / Pretreatment - Pressure: 0.007 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 298 K / Instrument: FEI VITROBOT MARK IV
Details: Wait time: 10 s Blot time: 2 s Blot force: -2 Drain time: 0 s.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Digitization - Dimensions - Width: 4096 pixel / Digitization - Dimensions - Height: 4096 pixel / Digitization - Sampling interval: 14.0 µm / Digitization - Frames/image: 1-7 / Number grids imaged: 1 / Number real images: 2369 / Average exposure time: 0.5 sec. / Average electron dose: 22.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 3.0 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 75000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 4515
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

3752

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 19.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine / Number images used: 3825
Initial angle assignmentType: PROJECTION MATCHING
Projection matching processing - Angular sampling: 7.5 degrees
Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) / Software - details: 3dautorefine
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: OTHER

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