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- EMDB-5676: Obstruction of Dengue Virus Maturation by Fab Fragments of the 2H... -

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Entry
Database: EMDB / ID: EMD-5676
TitleObstruction of Dengue Virus Maturation by Fab Fragments of the 2H2 Antibody
Map dataHigh-concentration 2H2 Fab complexed to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
Sample
  • Sample: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
  • Virus: Dengue virus
KeywordsDengue Maturation / Immature Dengue Antibody
Biological speciesDengue virus
Methodsingle particle reconstruction / cryo EM / Resolution: 21.0 Å
AuthorsWang Z / Li L / Penningtona JG / Sheng J / Yap M / Plevk P / Meng G / Sun L / Jiang W / Rossmann MG
CitationJournal: J Virol / Year: 2013
Title: Obstruction of dengue virus maturation by Fab fragments of the 2H2 antibody.
Authors: Zhiqing Wang / Long Li / Janice G Pennington / Ju Sheng / Moh Lan Yap / Pavel Plevka / Geng Meng / Lei Sun / Wen Jiang / Michael G Rossmann /
Abstract: The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature ...The 2H2 monoclonal antibody recognizes the precursor peptide on immature dengue virus and might therefore be a useful tool for investigating the conformational change that occurs when the immature virus enters an acidic environment. During dengue virus maturation, spiky, immature, noninfectious virions change their structure to form smooth-surfaced particles in the slightly acidic environment of the trans-Golgi network, thereby allowing cellular furin to cleave the precursor-membrane proteins. The dengue virions become fully infectious when they release the cleaved precursor peptide upon reaching the neutral-pH environment of the extracellular space. Here we report on the cryo-electron microscopy structures of the immature virus complexed with the 2H2 antigen binding fragments (Fab) at different concentrations and under various pH conditions. At neutral pH and a high concentration of Fab molecules, three Fab molecules bind to three precursor-membrane proteins on each spike of the immature virus. However, at a low concentration of Fab molecules and pH 7.0, only two Fab molecules bind to each spike. Changing to a slightly acidic pH caused no detectable change of structure for the sample with a high Fab concentration but caused severe structural damage to the low-concentration sample. Therefore, the 2H2 Fab inhibits the maturation process of immature dengue virus when Fab molecules are present at a high concentration, because the three Fab molecules on each spike hold the precursor-membrane molecules together, thereby inhibiting the normal conformational change that occurs during maturation.
History
DepositionMay 22, 2013-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 3, 2013-
UpdateAug 14, 2013-
Current statusAug 14, 2013Processing site: RCSB / Status: Released

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Structure visualization

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

emd_5676_1.jpg

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Map

FileDownload / File: emd_5676.map.gz / Format: CCP4 / Size: 51.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHigh-concentration 2H2 Fab complexed to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
Voxel sizeX=Y=Z: 3.72 Å
Density
Contour LevelBy EMDB: 2.0 / Movie #1: 3
Minimum - Maximum-5.24535704 - 14.54312992
Average (Standard dev.)0.52875352 (±1.89621508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-120-120-120
Dimensions240240240
Spacing240240240
CellA=B=C: 892.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.723.723.72
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z892.800892.800892.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-132-122-147
NX/NY/NZ250274261
MAP C/R/S123
start NC/NR/NS-120-120-120
NC/NR/NS240240240
D min/max/mean-5.24514.5430.529

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Supplemental data

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Sample components

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Entire : High-concentration Fab Fragment of 2H2 antibody binding to immatu...

EntireName: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
Components
  • Sample: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
  • Virus: Dengue virus

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Supramolecule #1000: High-concentration Fab Fragment of 2H2 antibody binding to immatu...

SupramoleculeName: High-concentration Fab Fragment of 2H2 antibody binding to immature Dengue virus back-neutralized to pH 7 after lowering to pH 6
type: sample / ID: 1000
Oligomeric state: Three Fab fragments bind to three pr on each trimeric spike
Number unique components: 3

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Supramolecule #1: Dengue virus

SupramoleculeName: Dengue virus / type: virus / ID: 1 / Details: immature virus / NCBI-ID: 12637 / Sci species name: Dengue virus / Sci species strain: P16881 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Aedes albopictus (Asian tiger mosquito) / Strain: C6/36 / synonym: INVERTEBRATES
Virus shellShell ID: 1 / Name: prM and E / Diameter: 600 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: 7 / Details: 100mM phosphate buffer
GridDetails: Quantifoil 200 mesh
VitrificationCryogen name: ETHANE / Chamber temperature: 100 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51040 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
TemperatureMin: 80 K / Max: 105 K / Average: 100 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
DateMar 8, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON COOLSCAN / Digitization - Sampling interval: 6 µm / Number real images: 47 / Average electron dose: 25 e/Å2

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Image processing

CTF correctionDetails: Film
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 21.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN2 / Number images used: 344

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Atomic model buiding 1

Initial modelPDB ID:

3c6d

SoftwareName: EMFit
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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