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- EMDB-63763: Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain b... -

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Basic information

Entry
Database: EMDB / ID: EMD-63763
TitleCryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with J9 fab
Map dataIcosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1 fab main map
Sample
  • Complex: dengue virus type 2 bound with J9 fab
    • Complex: monoclonal antibody J9
      • Protein or peptide: J9 heavy chain variable region
      • Protein or peptide: J9 Light chain variable region
    • Virus: dengue virus type 2
      • Protein or peptide: Membrane glycoprotein
      • Protein or peptide: Envelope Glycoprotein
KeywordsAntibody binding / fab-virus complex / E-protein / neutralization / VIRUS
Biological speciesHomo sapiens (human) / dengue virus type 2
Methodsingle particle reconstruction / cryo EM / Resolution: 7.21 Å
AuthorsRoy A / Prasad VM
Funding support India, 2 items
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 VM
History
DepositionMar 14, 2025-
Header (metadata) releaseApr 1, 2026-
Map releaseApr 1, 2026-
UpdateApr 1, 2026-
Current statusApr 1, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63763.png

Downloads & links

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Map

FileDownload / File: emd_63763.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationIcosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1 fab main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesX (Sec.)Y (Row.)Z (Col.)
2.32 Å/pix.
x 400 pix.
= 928. Å		2.32 Å/pix.
x 400 pix.
= 928. Å		2.32 Å/pix.
x 400 pix.
= 928. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 2.42
Minimum - Maximum-6.3082476 - 18.575431999999999
Average (Standard dev.)-0.000000000001904 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 928.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63763_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1...

Fileemd_63763_half_map_1.map
AnnotationIcosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1 fab half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Icosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1...

Fileemd_63763_half_map_2.map
AnnotationIcosahedral reconstruction of DENV2 THSTI/TRC/01 bound with J9V1 fab half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : dengue virus type 2 bound with J9 fab

EntireName: dengue virus type 2 bound with J9 fab
Components
  • Complex: dengue virus type 2 bound with J9 fab
    • Complex: monoclonal antibody J9
      • Protein or peptide: J9 heavy chain variable region
      • Protein or peptide: J9 Light chain variable region
    • Virus: dengue virus type 2
      • Protein or peptide: Membrane glycoprotein
      • Protein or peptide: Envelope Glycoprotein

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Supramolecule #1: dengue virus type 2 bound with J9 fab

SupramoleculeName: dengue virus type 2 bound with J9 fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Cultured in C6/36 mosquito cell lines and purified from cell supernatent

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Supramolecule #3: monoclonal antibody J9

SupramoleculeName: monoclonal antibody J9 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#4
Details: Fab fragment generated from papain based proteolytic cleavage of J9 IgG1.
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #2: dengue virus type 2

SupramoleculeName: dengue virus type 2 / type: virus / ID: 2 / Parent: 1 / Macromolecule list: #1-#2 / NCBI-ID: 11060 / Sci species name: dengue virus type 2 / Sci species strain: DENV2/THSTI/TRC/01 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Membrane glycoprotein

MacromoleculeName: Membrane glycoprotein / type: protein_or_peptide / ID: 1 / Details: sequence refers to UNZ79673.1 genebank / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: THSTI/TRC/01
Molecular weightTheoretical: 8.398842 KDa
SequenceString:
SVALVPHVGM GLETRTETWM SSEGAWKHAQ RIETWILRHP GFTIMAAILA YTIGTTYFQR VLIFILLTAV APSMT

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Macromolecule #2: Envelope Glycoprotein

MacromoleculeName: Envelope Glycoprotein / type: protein_or_peptide / ID: 2 / Details: sequence refers to UNZ79673.1 genebank / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: THSTI/TRC/01
Molecular weightTheoretical: 54.262562 KDa
SequenceString: MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KQPATLRKYC IEAKLTNTTT ASRCPTQGEP SLNEEQDKR FVCKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKI VQPENLEYTI VITPHSGEEN AVGNDTGKHG K EVKVTPQS ...String:
MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KQPATLRKYC IEAKLTNTTT ASRCPTQGEP SLNEEQDKR FVCKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKI VQPENLEYTI VITPHSGEEN AVGNDTGKHG K EVKVTPQS SITEAELTGY GTVTMECSPR TGLDFNEMVL LQMENKAWLV HRQWFLDLPL PWLPGADTQG SNWIQKETLV TF KNPHAKK QDVVVLGSQE GAMHTALTGA TEIQMSSGNL LFTGHLKCRL RMDKLQLKGM SYSMCTGKFK VVKEIAETQH GTI VIRVQY EGDGSPCKIP FEIMDLEKRH VLGRLITVNP IVTEKDSPVN IEAEPPFGDS YIIIGVEPGQ LKLSWFKKGS SIGQ MFETT MRGAKRMAIL GDTAWDFGSL GGVFTSIGKA LHQVFGAIYG AAFSGVSWTM KILIGVVITW IGMNSRSTSL SVSLV LVGV VTLYLGVMVQ A

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Macromolecule #3: J9 heavy chain variable region

MacromoleculeName: J9 heavy chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 12.754069 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
AEVRKPGSSV KVSCKTSGGS LNSYGISWVR QAPGGQGLEW MGGIIPFFGT VIYSDNYQGR ASFSSDESTT TAYMELRSLR SEDTAVYYC ARYCYSASCY HNWFDPWGQG TLVTVST

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Macromolecule #4: J9 Light chain variable region

MacromoleculeName: J9 Light chain variable region / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.333625 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
VLTQSPATLS LSPGERATLS CRASQSVGSS LAWYQQKPGQ APRLLIYDAS KRASGFPARF SGSGSGTDFT LTISSLEPGD FAVYYCQQR SSWPPYMYTF GQGTKL

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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
Component:
ConcentrationFormulaName
10.0 mMTris-HCLNTE buffer
120.0 mMNaClNTE buffer
1.0 mMEDTANTE buffer
GridModel: PELCO Ultrathin Carbon with Lacey Carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: LACEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV
DetailsDENV2 virus and J9V1 fab mixture with Fab in greater amount.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 1018 / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.75 µm / Nominal defocus min: 1.25 µm / Nominal magnification: 36000
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 10108
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: 3D-sphere geometry
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 7.21 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 668
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0) / Details: Maximum Likelihood
Final 3D classificationNumber classes: 6 / Avg.num./class: 1684 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: SwissModel, initial_model_type: in silico modelDENV2 Edimer
source_name: AlphaFold, initial_model_type: in silico modelJ9V1 fab
Detailsmap-correlation= 0.9013
RefinementProtocol: RIGID BODY FIT / Target criteria: map correlation
Output model

PDB-9mb0:
Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with J9 fab

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