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- EMDB-63762: Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particle... -

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Basic information

Entry
Database: EMDB / ID: EMD-63762
TitleHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with J9 fab
Map dataHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles 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: Envelope Glycoprotein E
Keywordsdengue virus / neutralizing antibody / fab-virus complex / E-protein / helical / VIRUS / VIRAL PROTEIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / 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 ...symbiont-mediated suppression of host JAK-STAT cascade via inhibition of host TYK2 activity / host cell mitochondrion / 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 / Immunoglobulin E-set / helicase superfamily c-terminal domain / 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
Methodhelical reconstruction / cryo EM / Resolution: 38.5 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_63762.png

Downloads & links

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Map

FileDownload / File: emd_63762.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with J9V1 fab main map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.4 Å/pix.
x 140 pix.
= 616. Å		4.4 Å/pix.
x 140 pix.
= 616. Å		4.4 Å/pix.
x 140 pix.
= 616. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.033
Minimum - Maximum-0.012283218 - 0.049971692
Average (Standard dev.)0.004109336 (±0.01002862)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 616.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_63762_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound...

Fileemd_63762_half_map_1.map
AnnotationHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles 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: Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound...

Fileemd_63762_half_map_2.map
AnnotationHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles 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: Envelope Glycoprotein E

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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: #2-#3
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 / 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: 2 / 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: J9 Heavy chain variable region

MacromoleculeName: J9 Heavy chain variable region / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.616318 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: QVQLVQSGAE VRKPGSSVKV SCKTSGGSLN SYGISWVRQA PGGQGLEWMG GIIPFFGTVI YSDNYQGRAS FSSDESTTTA YMELRSLRS EDTAVYYCAR YCYSASCYHN WFDPWGQGTL VTVSTASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ...String:
QVQLVQSGAE VRKPGSSVKV SCKTSGGSLN SYGISWVRQA PGGQGLEWMG GIIPFFGTVI YSDNYQGRAS FSSDESTTTA YMELRSLRS EDTAVYYCAR YCYSASCYHN WFDPWGQGTL VTVSTASTKG PSVFPLAPSS KSTSGGTAAL GCLVKDYFPE P VTVSWNSG ALTSGVHTFP AVLQSSGLYS LSSVVTVPSS SLGTQTYICN VNHKPSNTKV DKKV

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Macromolecule #3: J9 Light chain variable region

MacromoleculeName: J9 Light chain variable region / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 23.693346 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString: DIVLTQSPAT LSLSPGERAT LSCRASQSVG SSLAWYQQKP GQAPRLLIYD ASKRASGFPA RFSGSGSGTD FTLTISSLEP GDFAVYYCQ QRSSWPPYMY TFGQGTKLEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE ...String:
DIVLTQSPAT LSLSPGERAT LSCRASQSVG SSLAWYQQKP GQAPRLLIYD ASKRASGFPA RFSGSGSGTD FTLTISSLEP GDFAVYYCQ QRSSWPPYMY TFGQGTKLEI KRTVAAPSVF IFPPSDEQLK SGTASVVCLL NNFYPREAKV QWKVDNALQS G NSQESVTE QDSKDSTYSL SSTLTLSKAD YEKHKVYACE VTHQGLSSPV TKSFNRGEC

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical 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
DetailsDENV2 virus and J9V1 fab mixture with Fab in greater amount.

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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

Final reconstructionNumber classes used: 1
Applied symmetry - Helical parameters - Δz: 12.83 Å
Applied symmetry - Helical parameters - Δ&Phi: 35.83 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 38.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 4.0.1) / Number images used: 253
CTF correctionType: NONE
Segment selectionNumber selected: 2450 / Software - Name: RELION (ver. 4.0.1) / Software - details: Manual helical Picking
Startup modelType of model: OTHER / Details: molmap of Edimers arranged in a 3D helical rise
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0.1) / Details: Maximum Likelihood
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 J9V1 fab
DetailsPlacement of Edimer and fab according to density
RefinementProtocol: OTHER
Output model

PDB-9maz:
Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with J9 fab

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