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- EMDB-2998: Cryo-EM structure of the unexpanded particles of Dengue virus ser... -

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Entry
Database: EMDB / ID: EMD-2998
TitleCryo-EM structure of the unexpanded particles of Dengue virus serotype 2 strain New Guinea-C in complex with human antibody 2D22 Fab at 37 degrees C. The Fab molecules were added to the virus that had been pre-incubated at 37 degrees C.
Map dataReconstruction of the unexpanded particles of Dengue virus serotype 2 strain New Guinea-C in complex with human antibody 2D22 Fab at 37 degrees C. The Fab molecules were added to the virus that had been pre-incubated at 37 degrees C
Sample
  • Sample: Dengue virus serotype 2 strain New Guinea-C in complex with Fab fragments of human antibody 2D22.
  • Virus: Dengue Virus serotype 2
  • Protein or peptide: Antigen-binding fragment of human antibody 2D22
Keywordsdengue virus / human antibody / cryo-EM / neutralization
Biological speciesHomo sapiens (human) / Dengue Virus serotype 2
Methodsingle particle reconstruction / cryo EM / Resolution: 11.0 Å
AuthorsFibriansah G / Ibarra KD / Ng TS / Smith SA / Tan JL / Lim XN / Ooi JSG / Kostyuchenko VA / Wang J / de Silva AM ...Fibriansah G / Ibarra KD / Ng TS / Smith SA / Tan JL / Lim XN / Ooi JSG / Kostyuchenko VA / Wang J / de Silva AM / Harris E / Crowe JE / Lok SM
CitationJournal: Science / Year: 2015
Title: DENGUE VIRUS. Cryo-EM structure of an antibody that neutralizes dengue virus type 2 by locking E protein dimers.
Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / ...Authors: Guntur Fibriansah / Kristie D Ibarra / Thiam-Seng Ng / Scott A Smith / Joanne L Tan / Xin-Ni Lim / Justin S G Ooi / Victor A Kostyuchenko / Jiaqi Wang / Aravinda M de Silva / Eva Harris / James E Crowe / Shee-Mei Lok /
Abstract: There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. ...There are four closely-related dengue virus (DENV) serotypes. Infection with one serotype generates antibodies that may cross-react and enhance infection with other serotypes in a secondary infection. We demonstrated that DENV serotype 2 (DENV2)-specific human monoclonal antibody (HMAb) 2D22 is therapeutic in a mouse model of antibody-enhanced severe dengue disease. We determined the cryo-electron microscopy (cryo-EM) structures of HMAb 2D22 complexed with two different DENV2 strains. HMAb 2D22 binds across viral envelope (E) proteins in the dimeric structure, which probably blocks the E protein reorganization required for virus fusion. HMAb 2D22 "locks" two-thirds of or all dimers on the virus surface, depending on the strain, but neutralizes these DENV2 strains with equal potency. The epitope defined by HMAb 2D22 is a potential target for vaccines and therapeutics.
History
DepositionMay 7, 2015-
Header (metadata) releaseMay 20, 2015-
Map releaseJul 15, 2015-
UpdateJul 15, 2015-
Current statusJul 15, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_2998.png

Downloads & links

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Map

FileDownload / File: emd_2998.map.gz / Format: CCP4 / Size: 500 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the unexpanded particles of Dengue virus serotype 2 strain New Guinea-C in complex with human antibody 2D22 Fab at 37 degrees C. The Fab molecules were added to the virus that had been pre-incubated at 37 degrees C
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.69 Å/pix.
x 512 pix.
= 865.28 Å		1.69 Å/pix.
x 512 pix.
= 865.28 Å		1.69 Å/pix.
x 512 pix.
= 865.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.69 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.0 / Movie #1: 3
Minimum - Maximum-12.474801060000001 - 11.283245089999999
Average (Standard dev.)-0.032467 (±0.97553211)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-256-256-256
Dimensions512512512
Spacing512512512
CellA=B=C: 865.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.691.691.69
M x/y/z512512512
origin x/y/z0.0000.0000.000
length x/y/z865.280865.280865.280
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S123
start NC/NR/NS-256-256-256
NC/NR/NS512512512
D min/max/mean-12.47511.283-0.032

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Supplemental data

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Sample components

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Entire : Dengue virus serotype 2 strain New Guinea-C in complex with Fab f...

EntireName: Dengue virus serotype 2 strain New Guinea-C in complex with Fab fragments of human antibody 2D22.
Components
  • Sample: Dengue virus serotype 2 strain New Guinea-C in complex with Fab fragments of human antibody 2D22.
  • Virus: Dengue Virus serotype 2
  • Protein or peptide: Antigen-binding fragment of human antibody 2D22

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Supramolecule #1000: Dengue virus serotype 2 strain New Guinea-C in complex with Fab f...

SupramoleculeName: Dengue virus serotype 2 strain New Guinea-C in complex with Fab fragments of human antibody 2D22.
type: sample / ID: 1000
Details: The Fab molecules were added to the virus that had been pre-incubated at 37 degrees C
Number unique components: 2

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Supramolecule #1: Dengue Virus serotype 2

SupramoleculeName: Dengue Virus serotype 2 / type: virus / ID: 1 / Sci species name: Dengue Virus serotype 2 / Sci species strain: New Guinea-C / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Host systemOrganism: Aedes albopictus (Asian tiger mosquito) / Recombinant cell: C6/36

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Macromolecule #1: Antigen-binding fragment of human antibody 2D22

MacromoleculeName: Antigen-binding fragment of human antibody 2D22 / type: protein_or_peptide / ID: 1
Details: 180 copies of Fab 2D22 molecule bind to virus surface
Number of copies: 180 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human / Cell: memory B-cell
Molecular weightTheoretical: 50 KDa

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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: 10 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA
GridDetails: ultra-thin carbon-coated lacey carbon grid
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV
Method: blotted with filter paper for 2 seconds prior to snap freezing

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJun 14, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 184 / Average electron dose: 20 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 0.0046 µm / Nominal defocus min: 0.0019 µm / Nominal magnification: 47000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsThe particles were manually selected
CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.0 Å / Resolution method: OTHER / Software - Name: EMAN, EMAN2, MPSA / Number images used: 982

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