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- EMDB-63759: Cryo-EM structure of Dengue virus serotype2 US/BID-V594/2006 stra... -

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Entry
Database: EMDB / ID: EMD-63759
TitleCryo-EM structure of Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab.
Map dataDENV 2 US/HBID-V594/2006 J9V1 fab complex deepemhancer sharpened map
Sample
  • Complex: Dengue virus serotype2 US/BID-V594/2006 strain 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: Envelope Glycoprotein E
      • Protein or peptide: Membrane Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose
KeywordsDengue virus / broadly neutralizing antibody / fab-virus complex / E-protein / flavivirus / VIRUS
Function / homology
Function and homology information


host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell ...host cell mitochondrion / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / symbiont-mediated suppression of host JAK-STAT cascade via inhibition of STAT2 activity / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of MAVS activity / viral capsid / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / molecular adaptor activity / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell perinuclear region of cytoplasm / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / serine-type endopeptidase activity / symbiont-mediated activation of host autophagy / viral RNA genome replication / RNA-directed RNA polymerase activity / fusion of virus membrane with host endosome membrane / viral envelope / lipid binding / virion attachment to host cell / host cell nucleus / virion membrane / structural molecule activity / proteolysis / extracellular region / ATP binding / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus non-structural protein NS4B / mRNA cap 0/1 methyltransferase / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus capsid protein C / Flavivirus capsid protein C / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M superfamily, flavivirus / Envelope glycoprotein M, flavivirus / Flavivirus polyprotein propeptide superfamily / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Ribosomal RNA methyltransferase, FtsJ domain / FtsJ-like methyltransferase / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / DEAD box, Flavivirus / Flavivirus DEAD domain / helicase superfamily c-terminal domain / Immunoglobulin E-set / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human) / dengue virus type 2
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 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_63759.png

Downloads & links

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Map

FileDownload / File: emd_63759.map.gz / Format: CCP4 / Size: 1.9 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDENV 2 US/HBID-V594/2006 J9V1 fab complex deepemhancer sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 800 pix.
= 880. Å		1.1 Å/pix.
x 800 pix.
= 880. Å		1.1 Å/pix.
x 800 pix.
= 880. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0273
Minimum - Maximum-0.042825054 - 1.8694766
Average (Standard dev.)0.0034397403 (±0.04086339)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions800800800
Spacing800800800
CellA=B=C: 880.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63759_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DENV 2 US/HBID-V594/2006 J9V1 fab complex half map 2

Fileemd_63759_half_map_1.map
AnnotationDENV 2 US/HBID-V594/2006 J9V1 fab complex half map 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: DENV 2 US/HBID-V594/2006 J9V1 fab complex half map 1

Fileemd_63759_half_map_2.map
AnnotationDENV 2 US/HBID-V594/2006 J9V1 fab complex half map 1
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 serotype2 US/BID-V594/2006 strain bound with J9 fab

EntireName: Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab
Components
  • Complex: Dengue virus serotype2 US/BID-V594/2006 strain 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: Envelope Glycoprotein E
      • Protein or peptide: Membrane Glycoprotein
  • Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose

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Supramolecule #1: Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab

SupramoleculeName: Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4
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: DENV-2/US/BID-V594/2006 / Virus type: VIRION / Virus isolate: SEROTYPE / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Envelope Glycoprotein E

MacromoleculeName: Envelope Glycoprotein E / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: DENV-2/US/BID-V594/2006
Molecular weightTheoretical: 54.413789 KDa
SequenceString: MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KQPATLRKYC IEAKLTNTTT ESRCPTQGEP SLNEEQDKR FICKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKV VLPENLEYTI VITPHSGEEH AVGNDTGKHG K EIKITPQS ...String:
MRCIGISNRD FVEGVSGGSW VDIVLEHGSC VTTMAKNKPT LDFELIKTEA KQPATLRKYC IEAKLTNTTT ESRCPTQGEP SLNEEQDKR FICKHSMVDR GWGNGCGLFG KGGIVTCAMF TCKKNMEGKV VLPENLEYTI VITPHSGEEH AVGNDTGKHG K EIKITPQS SITEAELTGY GTVTMECSPR TGLDFNEMVL LQMEDKAWLV HRQWFLDLPL PWLPGADTQG SNWIQKETLV TF KNPHAKK QDVVVLGSQE GAMHTALTGA TEIQMSSGNL LFTGHLKCRL RMDKLQLKGM SYSMCTGKFK IVKEIAETQH GTI VIRVQY EGDGSPCKIP FEIMDLEKRH VLGRLITVNP IVTEKDSPVN IEAEPPFGDS YIIIGVEPGQ LKLNWFKKGS SIGQ MFETT MRGAKRMAIL GDTAWDFGSL GGVFTSIGKA LHQVFGAIYG AAFSGVSWTM KILIGVIITW IGMNSRSTSL SVSLV LVGV VTLYLGVMVQ A

UniProtKB: Genome polyprotein

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Macromolecule #2: Membrane Glycoprotein

MacromoleculeName: Membrane Glycoprotein / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: dengue virus type 2 / Strain: DENV-2/US/BID-V594/2006
Molecular weightTheoretical: 8.373814 KDa
SequenceString:
SVALVPHVGM GLETRTETWM SSEGAWKHVQ RIETWILRHP GFTIMAAILA YTIGTTHFQR ALIFILLTAV APSMT

UniProtKB: Genome polyprotein

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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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Macromolecule #8: 2-acetamido-2-deoxy-beta-D-glucopyranose

MacromoleculeName: 2-acetamido-2-deoxy-beta-D-glucopyranose / type: ligand / ID: 8 / Number of copies: 1 / Formula: NAG
Molecular weightTheoretical: 221.208 Da
Chemical component information

ChemComp-NAG:
2-acetamido-2-deoxy-beta-D-glucopyranose

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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: LEICA EM GP / Details: GP2.
DetailsDENV2 virus and J9 fab complex

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4756 / Average electron dose: 40.3 e/Å2
Details: Images were collected in counting mode and dose fractionated into 38 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 81000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 15000
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: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.6.0) / Number images used: 2903
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: 3 / Avg.num./class: 1500 / Software - Name: cryoSPARC (ver. 4.6.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
ChainDetails
source_name: SwissModel, initial_model_type: in silico modelfor DENV2 E-protein
source_name: AlphaFold, initial_model_type: in silico modelfor J9 fab
RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-9mav:
Cryo-EM structure of Dengue virus serotype2 US/BID-V594/2006 strain bound with J9 fab.

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