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- PDB-9mb0: Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain b... -

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Basic information

Entry
Database: PDB / ID: 9mb0
TitleCryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with J9 fab
Components
  • Envelope Glycoprotein
  • J9 Light chain variable region
  • J9 heavy chain variable region
  • Membrane glycoprotein
KeywordsVIRUS / Antibody binding / fab-virus complex / E-protein / neutralization
Biological speciesHomo sapiens (human)
dengue virus type 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 7.21 Å
AuthorsRoy, A. / Prasad, V.M.
Funding support India, 2items
OrganizationGrant numberCountry
Science and Engineering Research Board (SERB)SPG/2021/002433 India
Department of Biotechnology (DBT, India)IA/I/22/1/506233 India
CitationJournal: To Be Published
Title: Structural determinants of broadly neutralizing human antibodies binding to morphological dengue virus variants.
Authors: Chatterjee, A. / Roy, A. / Srinivasan, S. / Charles, S. / Lubow, J. / Goo, L. / Prasad, V.M.
History
DepositionMar 14, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Apr 1, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: Membrane glycoprotein
A: Envelope Glycoprotein
D: Membrane glycoprotein
C: Envelope Glycoprotein
F: Membrane glycoprotein
E: Envelope Glycoprotein
H: J9 heavy chain variable region
L: J9 Light chain variable region
K: J9 heavy chain variable region
M: J9 Light chain variable region


Theoretical massNumber of molelcules
Total (without water)236,16010
Polymers236,16010
Non-polymers00
Water00
1
B: Membrane glycoprotein
A: Envelope Glycoprotein
D: Membrane glycoprotein
C: Envelope Glycoprotein
F: Membrane glycoprotein
E: Envelope Glycoprotein
H: J9 heavy chain variable region
L: J9 Light chain variable region
K: J9 heavy chain variable region
M: J9 Light chain variable region
x 60


Theoretical massNumber of molelcules
Total (without water)14,169,576600
Polymers14,169,576600
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

#1: Protein Membrane glycoprotein


Mass: 8398.842 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: sequence refers to UNZ79673.1 genebank / Source: (natural) dengue virus type 2 / Cell line: C6/36 / Plasmid details: Cell supernatent / Strain: THSTI/TRC/01
#2: Protein Envelope Glycoprotein


Mass: 54262.562 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Details: sequence refers to UNZ79673.1 genebank / Source: (natural) dengue virus type 2 / Cell line: C6/36 / Plasmid details: Cell supernatent / Strain: THSTI/TRC/01
#3: Antibody J9 heavy chain variable region


Mass: 12754.069 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral blood mononuclear cells / Gene: J9 heavy chain variable / Cell line (production host): Expi293f / Production host: Homo sapiens (human)
#4: Antibody J9 Light chain variable region


Mass: 11333.625 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral blood mononuclear cells / Gene: J9 light chain variable / Cell line (production host): Expi293f / Production host: Homo sapiens (human)
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeDetailsEntity IDParent-IDSource
1dengue virus type 2 bound with J9 fabCOMPLEXCultured in C6/36 mosquito cell lines and purified from cell supernatentall0MULTIPLE SOURCES
2dengue virus type 2VIRUS#1-#21NATURAL
3monoclonal antibody J9COMPLEXFab fragment generated from papain based proteolytic cleavage of J9 IgG1.#3-#41RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12dengue virus type 211060DENV2/THSTI/TRC/01
23Homo sapiens (human)9606
Source (recombinant)Organism: Homo sapiens (human) / Cell: Expi293f
Details of virusEmpty: NO / Enveloped: YES / Isolate: SEROTYPE / Type: VIRION
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 8
Buffer component
IDConc.NameFormulaBuffer-ID
110 mMNTE bufferTris-HCL1
2120 mMNTE bufferNaCl1
31 mMNTE bufferEDTA1
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: DENV2 virus and J9V1 fab mixture with Fab in greater amount.
Specimen supportGrid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: PELCO Ultrathin Carbon with Lacey Carbon
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
MicroscopyModel: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 36000 X / Nominal defocus max: 2750 nm / Nominal defocus min: 1250 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 1018
Image scansMovie frames/image: 20

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Processing

EM software
IDNameVersionCategory
1RELION4.0.1particle selection
2Latitudeimage acquisition
4cryoSPARC4.6.0CTF correction
7UCSF Chimera1.17model fitting
9cryoSPARC4.6.0initial Euler assignment
10cryoSPARC4.6.0final Euler assignment
11RELION4.0.1classification
12cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 10108
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 7.21 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 668 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: map correlation / Details: map-correlation= 0.9013
Atomic model building
ID 3D fitting-IDDetailsSource nameType
11DENV2 EdimerSwissModelin silico model
21J9V1 fabAlphaFoldin silico model

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