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- PDB-9u34: Helical Reconstruction of DENV2 US/BID-V594/2006 tubular particle... -

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Basic information

Entry
Database: PDB / ID: 9u34
TitleHelical Reconstruction of DENV2 US/BID-V594/2006 tubular particles bound with D14.F25.S02 fab
Components
  • D14.F25.S02 Heavy chain
  • D14.F25.S02 Light chain
  • Envelope Glycoprotein E
  • Membrane Glycoprotein
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / dengue 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
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 14.7 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: Mask / Part number: 1 / Data content type: Mask / 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
C: Envelope Glycoprotein E
A: Envelope Glycoprotein E
L: D14.F25.S02 Light chain
H: D14.F25.S02 Heavy chain
B: Membrane Glycoprotein
D: Membrane Glycoprotein
M: D14.F25.S02 Light chain
K: D14.F25.S02 Heavy chain


Theoretical massNumber of molelcules
Total (without water)176,8968
Polymers176,8968
Non-polymers00
Water00
1
C: Envelope Glycoprotein E
A: Envelope Glycoprotein E
L: D14.F25.S02 Light chain
H: D14.F25.S02 Heavy chain
B: Membrane Glycoprotein
D: Membrane Glycoprotein
M: D14.F25.S02 Light chain
K: D14.F25.S02 Heavy chain
x 40


Theoretical massNumber of molelcules
Total (without water)7,075,851320
Polymers7,075,851320
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation39
MethodUCSF CHIMERA

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Components

#1: Protein Envelope Glycoprotein E


Mass: 54413.789 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) dengue virus type 2 / Cell line: C6/36 / Plasmid details: Cell supernatent / Strain: US/BID-V594/2006 / References: UniProt: B1PP76
#2: Antibody D14.F25.S02 Light chain


Mass: 11679.897 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral Blood Mononuclear Cell / Gene: D14.F25.S02 heavy chain / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody D14.F25.S02 Heavy chain


Mass: 13980.643 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line: Peripheral Blood Mononuclear Cell / Gene: D14.F25.S02 heavy chain / Cell line (production host): ExpiCHO / Production host: Cricetulus griseus (Chinese hamster)
#4: Protein Membrane Glycoprotein


Mass: 8373.814 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) dengue virus type 2 / Cell line: C6/36 / Plasmid details: Cell supernatent / Strain: US/BID-V594/2006 / References: UniProt: B1PP76
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: helical reconstruction

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Sample preparation

Component
IDNameTypeDetails (eV)Entity IDParent-IDSource
1dengue virus type 2 bound with D14.F25.S02 fabCOMPLEXCultured in C6/36 mosquito cell lines and purified from cell supernatentall0MULTIPLE SOURCES
2dengue virus type 2COMPLEX#1, #41NATURAL
3monoclonal antibody D14.F25.S02COMPLEXFab fragment generated from papain based proteolytic cleavage of D14.F25.S02 IgG1.#2-#31RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-IDStrain
12dengue virus type 211060DENV-2/US/BID-V594/2006
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.S02 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: LEICA EM GP / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 18787
Details: Images were collected in counting mode and dose fractionated into 38 frames.
EM imaging opticsEnergyfilter name: GIF Bioquantum / Energyfilter slit width: 20 eV

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1RELION4.0.1particle selectionManual helical Picking
2EPUimage acquisition
4cryoSPARC4.6.0CTF correction
7UCSF Chimera1.18model fitting
10cryoSPARC4.6.0initial Euler assignment
11cryoSPARC4.6.0final Euler assignment
12RELION4.0.1classification
13cryoSPARC4.6.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 29.48 ° / Axial rise/subunit: 11.25 Å / Axial symmetry: C1
Particle selectionNum. of particles selected: 4784
3D reconstructionResolution: 14.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 405 / Algorithm: FOURIER SPACE / Num. of class averages: 1 / Symmetry type: HELICAL
Atomic model buildingProtocol: RIGID BODY FIT / Target criteria: Map correlation / Details: correlation value= 0.93
Atomic model building
ID 3D fitting-IDDetails (eV)Source nameType
11for DENV2 E-proteinOtherin silico model
21for fabAlphaFoldin silico model

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