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- EMDB-2818: Dengue virus serotype 2 with Fab fragments of human antibody B7 -

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Basic information

Entry
Database: EMDB / ID: EMD-2818
TitleDengue virus serotype 2 with Fab fragments of human antibody B7
Map dataReconstruction of Dengue Virus Serotype 2 in complex with Human Antibody B7 Fab Fragment.
Sample
  • Sample: Fab Fragment of human antibody to Dengue 2 virus
  • Virus: Dengue virus 2
  • Protein or peptide: FAB
Keywordsdengue virus / human monoclonal antibody / potent broad neutralization / E-dimer Dependent epitope
Biological speciesHomo sapiens (human) / Dengue virus 2
Methodsingle particle reconstruction / cryo EM / Resolution: 10.24 Å
AuthorsDejnirattisai W / Wongwiwat W / Supasa S / Zhang X / Dai X / Rouvinsky A / Jumnainsong A / Edwards C / Quyen NT / Duangchinda T ...Dejnirattisai W / Wongwiwat W / Supasa S / Zhang X / Dai X / Rouvinsky A / Jumnainsong A / Edwards C / Quyen NT / Duangchinda T / Grimes JM / Tsai WY / Lai CY / Wang WK / Malasit P / Farrar J / Simmons CP / Zhou ZH / Rey FA / Mongkolsapaya J / Screaton GR
Citation
Journal: Nat Immunol / Year: 2015
Title: A new class of highly potent, broadly neutralizing antibodies isolated from viremic patients infected with dengue virus.
Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya ...Authors: Wanwisa Dejnirattisai / Wiyada Wongwiwat / Sunpetchuda Supasa / Xiaokang Zhang / Xinghong Dai / Alexander Rouvinski / Amonrat Jumnainsong / Carolyn Edwards / Nguyen Than Ha Quyen / Thaneeya Duangchinda / Jonathan M Grimes / Wen-Yang Tsai / Chih-Yun Lai / Wei-Kung Wang / Prida Malasit / Jeremy Farrar / Cameron P Simmons / Z Hong Zhou / Felix A Rey / Juthathip Mongkolsapaya / Gavin R Screaton /
Abstract: Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal ...Dengue is a rapidly emerging, mosquito-borne viral infection, with an estimated 400 million infections occurring annually. To gain insight into dengue immunity, we characterized 145 human monoclonal antibodies (mAbs) and identified a previously unknown epitope, the envelope dimer epitope (EDE), that bridges two envelope protein subunits that make up the 90 repeating dimers on the mature virion. The mAbs to EDE were broadly reactive across the dengue serocomplex and fully neutralized virus produced in either insect cells or primary human cells, with 50% neutralization in the low picomolar range. Our results provide a path to a subunit vaccine against dengue virus and have implications for the design and monitoring of future vaccine trials in which the induction of antibody to the EDE should be prioritized.
#1: Journal: NATURE
Title: Recognition determinants of broadly neutralizing human antibodies against dengue viruses
Authors: Rouvinski A / Guardado-Calvo P / Barba-Spaeth G / Duquerroy S / Vaney MC / Kikuti CM / Navarro Sanchez E / Dejnirattisai W / Wongwiwat W / Haouz A / Girard-Blanc C / Petres S / England P / ...Authors: Rouvinski A / Guardado-Calvo P / Barba-Spaeth G / Duquerroy S / Vaney MC / Kikuti CM / Navarro Sanchez E / Dejnirattisai W / Wongwiwat W / Haouz A / Girard-Blanc C / Petres S / England P / Supasa S / Shepard WE / Duangchinda T / Siridechadilok B / Despres P / Arenzana-Seisdedos F / Dussart P / Mongkolsapaya J / Screaton GR / Rey FA
History
DepositionNov 14, 2014-
Header (metadata) releaseDec 10, 2014-
Map releaseDec 10, 2014-
UpdateFeb 17, 2016-
Current statusFeb 17, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd-2818.png

Downloads & links

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Map

FileDownload / File: emd_2818.map.gz / Format: CCP4 / Size: 122.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of Dengue Virus Serotype 2 in complex with Human Antibody B7 Fab Fragment.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.56 Å/pix.
x 320 pix.
= 819.2 Å		2.56 Å/pix.
x 320 pix.
= 819.2 Å		2.56 Å/pix.
x 320 pix.
= 819.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-8.33887768 - 14.047575950000001
Average (Standard dev.)0.00544979 (±0.94821829)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 819.19995 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.562.562.56
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z819.200819.200819.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-8.33914.0480.005

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Supplemental data

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Sample components

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Entire : Fab Fragment of human antibody to Dengue 2 virus

EntireName: Fab Fragment of human antibody to Dengue 2 virus
Components
  • Sample: Fab Fragment of human antibody to Dengue 2 virus
  • Virus: Dengue virus 2
  • Protein or peptide: FAB

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Supramolecule #1000: Fab Fragment of human antibody to Dengue 2 virus

SupramoleculeName: Fab Fragment of human antibody to Dengue 2 virus / type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: Dengue virus 2

SupramoleculeName: Dengue virus 2 / type: virus / ID: 1 / NCBI-ID: 11060 / Sci species name: Dengue virus 2 / Sci species strain: NGC / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes aegypti (yellow fever mosquito) / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Diameter: 500 Å / T number (triangulation number): 3

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Macromolecule #1: FAB

MacromoleculeName: FAB / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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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: 7.4 / Details: PBS
GridDetails: 200 mesh quantifoil 2/2
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV / Method: Blot for 4 seconds before plunging

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Electron microscopy

MicroscopeFEI TITAN KRIOS
DateJun 9, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 5.0 µm / Number real images: 1000 / Average electron dose: 25 e/Å2
Details: Every image is the average of 25 frames recorded by the direct electron detector
Bits/pixel: 32
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.2 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 10.24 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Relion, EMAN2 / Number images used: 8000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

3j27


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D / Chain - #4 - Chain ID: E / Chain - #5 - Chain ID: F
SoftwareName: UCSF Chimera
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: cross coefficient

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