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- PDB-9u36: Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain b... -

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Basic information

Entry
Database: PDB / ID: 9u36
TitleCryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 fab
Components
  • D14.F25.S02 Heavy chain variable region
  • D14.F25.S02 Light chain variable region
  • Envelope Glycoprotein
  • 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: 19.08 Å
AuthorsChatterjee, 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 18, 2025Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 29, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 29, 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
A: Envelope Glycoprotein
B: Envelope Glycoprotein
C: Membrane glycoprotein
D: Membrane glycoprotein
H: D14.F25.S02 Heavy chain variable region
K: D14.F25.S02 Heavy chain variable region
L: D14.F25.S02 Light chain variable region
M: D14.F25.S02 Light chain variable region
E: Envelope Glycoprotein
F: Membrane glycoprotein
N: D14.F25.S02 Heavy chain variable region
O: D14.F25.S02 Light chain variable region


Theoretical massNumber of molelcules
Total (without water)264,96612
Polymers264,96612
Non-polymers00
Water00
1
A: Envelope Glycoprotein
B: Envelope Glycoprotein
C: Membrane glycoprotein
D: Membrane glycoprotein
H: D14.F25.S02 Heavy chain variable region
K: D14.F25.S02 Heavy chain variable region
L: D14.F25.S02 Light chain variable region
M: D14.F25.S02 Light chain variable region
E: Envelope Glycoprotein
F: Membrane glycoprotein
N: D14.F25.S02 Heavy chain variable region
O: D14.F25.S02 Light chain variable region
x 60


Theoretical massNumber of molelcules
Total (without water)15,897,950720
Polymers15,897,950720
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Envelope Glycoprotein
B: Envelope Glycoprotein
C: Membrane glycoprotein
D: Membrane glycoprotein
H: D14.F25.S02 Heavy chain variable region
K: D14.F25.S02 Heavy chain variable region
L: D14.F25.S02 Light chain variable region
M: D14.F25.S02 Light chain variable region
E: Envelope Glycoprotein
F: Membrane glycoprotein
N: D14.F25.S02 Heavy chain variable region
O: D14.F25.S02 Light chain variable region
x 5


  • icosahedral pentamer
  • 1.32 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,324,82960
Polymers1,324,82960
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Envelope Glycoprotein
B: Envelope Glycoprotein
C: Membrane glycoprotein
D: Membrane glycoprotein
H: D14.F25.S02 Heavy chain variable region
K: D14.F25.S02 Heavy chain variable region
L: D14.F25.S02 Light chain variable region
M: D14.F25.S02 Light chain variable region
E: Envelope Glycoprotein
F: Membrane glycoprotein
N: D14.F25.S02 Heavy chain variable region
O: D14.F25.S02 Light chain variable region
x 6


  • icosahedral 23 hexamer
  • 1.59 MDa, 72 polymers
Theoretical massNumber of molelcules
Total (without water)1,589,79572
Polymers1,589,79572
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: 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
#2: 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
#3: Antibody D14.F25.S02 Heavy chain variable region


Mass: 13980.643 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral Blood Mononuclear Cells / Gene: D14.F25.S02 heavy chain / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Antibody D14.F25.S02 Light chain variable region


Mass: 11679.897 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral Blood Mononuclear Cells / Gene: D14.F25.S02 light chain / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
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
IDNameTypeDetails (eV)Entity IDParent-IDSource
1dengue virus type 2 bound with D14.F25.SO2 fabCOMPLEXCell supernatentall0MULTIPLE SOURCES
2dengue virus type 2COMPLEX#1-#21NATURAL
3monoclonal antibody D14.F25.S02COMPLEXFab fragment generated from papain based proteolytic cleavage of D14.F25.S02 IgG1.#4, #31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12dengue virus type 211060THSTI/TRC/01
23Homo sapiens (human)9606
Source (recombinant)Organism: Cricetulus griseus (Chinese hamster) / Cell: ExpiCHO
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 D14.F25.SO2 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 / 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: 2 / Num. of real images: 4029
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: 26782
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 19.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 4715 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: map correlation
Details: Map fitting was done with fully symmetrized icosahedral atomic model. Map correlation value was 0.8293
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameType
11D14.F25.SO2 fabAlphaFoldin silico model
21DENV2 E-proteinSwissModelin silico model

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