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- EMDB-63811: Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain b... -

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Basic information

Entry
Database: EMDB / ID: EMD-63811
TitleCryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 fab
Map dataCryo-EM structure of DENV2 THSTI/TRC/01 bound with D14.F25.SO2 fab
Sample
  • Complex: dengue virus type 2 bound with D14.F25.SO2 fab
    • Complex: dengue virus type 2
      • Protein or peptide: Envelope Glycoprotein
      • Protein or peptide: Membrane glycoprotein
    • Complex: monoclonal antibody D14.F25.S02
      • Protein or peptide: D14.F25.S02 Light chain variable region
      • Protein or peptide: D14.F25.S02 Heavy chain variable region
KeywordsAntibody binding / fab-virus complex / E-protein / Neutralization / VIRUS
Biological speciesdengue virus type 2 / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.08 Å
AuthorsChatterjee 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 18, 2025-
Header (metadata) releaseApr 29, 2026-
Map releaseApr 29, 2026-
UpdateApr 29, 2026-
Current statusApr 29, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_63811.png

Downloads & links

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Map

FileDownload / File: emd_63811.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of DENV2 THSTI/TRC/01 bound with D14.F25.SO2 fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.32 Å/pix.
x 512 pix.
= 1187.84 Å		2.32 Å/pix.
x 512 pix.
= 1187.84 Å		2.32 Å/pix.
x 512 pix.
= 1187.84 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: 0.138
Minimum - Maximum-0.2257163 - 0.49222207
Average (Standard dev.)0.0013367502 (±0.055534888)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 1187.84 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: half map

Fileemd_63811_half_map_1.map
Annotationhalf map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map

Fileemd_63811_half_map_2.map
Annotationhalf 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 D14.F25.SO2 fab

EntireName: dengue virus type 2 bound with D14.F25.SO2 fab
Components
  • Complex: dengue virus type 2 bound with D14.F25.SO2 fab
    • Complex: dengue virus type 2
      • Protein or peptide: Envelope Glycoprotein
      • Protein or peptide: Membrane glycoprotein
    • Complex: monoclonal antibody D14.F25.S02
      • Protein or peptide: D14.F25.S02 Light chain variable region
      • Protein or peptide: D14.F25.S02 Heavy chain variable region

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Supramolecule #1: dengue virus type 2 bound with D14.F25.SO2 fab

SupramoleculeName: dengue virus type 2 bound with D14.F25.SO2 fab / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: Cell supernatent

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Supramolecule #2: dengue virus type 2

SupramoleculeName: dengue virus type 2 / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2
Source (natural)Organism: dengue virus type 2 / Strain: THSTI/TRC/01

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Supramolecule #3: monoclonal antibody D14.F25.S02

SupramoleculeName: monoclonal antibody D14.F25.S02 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #4, #3
Details: Fab fragment generated from papain based proteolytic cleavage of D14.F25.S02 IgG1.
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope Glycoprotein

MacromoleculeName: Envelope 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: 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 #2: Membrane glycoprotein

MacromoleculeName: Membrane 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: 8.398842 KDa
SequenceString:
SVALVPHVGM GLETRTETWM SSEGAWKHAQ RIETWILRHP GFTIMAAILA YTIGTTYFQR VLIFILLTAV APSMT

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Macromolecule #3: D14.F25.S02 Heavy chain variable region

MacromoleculeName: D14.F25.S02 Heavy chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.980643 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QVQLVQSGAE VKKPGSSAKV SCKASGGTFS SYAISWVRQA PGQGLEWMGS IMPIFGTVNY AQKFQGRVTI TADESTSTAY MELSRLRSE DTAVYFCARG WGGNYRSADL WIYFDLWGQG TLVTVSSRS

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Macromolecule #4: D14.F25.S02 Light chain variable region

MacromoleculeName: D14.F25.S02 Light chain variable region / type: protein_or_peptide / ID: 4 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.679897 KDa
Recombinant expressionOrganism: Cricetulus griseus (Chinese hamster)
SequenceString:
QSALTQPRSV SGSPGQSVTI SCTGTSSDVG GYKYVSWYQQ HPGKAPKLMI YDVTKRPSGV PDRFSGSKSG NTASLTISGL QADDEADYY CCSYAGSYTH VVFGGGTKLT VL

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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 D14.F25.SO2 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: 2 / Number real images: 4029 / 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 / 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: 26782
CTF correctionSoftware - Name: cryoSPARC (ver. 4.6.0) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: 3D-sphere
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: I (icosahedral) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 19.08 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 4715
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.6.0)
Final 3D classificationNumber classes: 4 / Avg.num./class: 1694 / Software - Name: RELION (ver. 4.0.1)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: AlphaFold, initial_model_type: in silico modelD14.F25.SO2 fab
source_name: SwissModel, initial_model_type: in silico modelDENV2 E-protein
DetailsMap fitting was done with fully symmetrized icosahedral atomic model. Map correlation value was 0.8293
RefinementProtocol: RIGID BODY FIT / Target criteria: map correlation
Output model

PDB-9u36:
Cryo-EM structure of Dengue virus serotype2 THSTI/TRC/01 strain bound with D14.F25.SO2 fab

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