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- PDB-8jn3: Cryo-EM structure of dengue virus serotype 3 strain 863DK in comp... -

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Basic information

Entry
Database: PDB / ID: 8jn3
TitleCryo-EM structure of dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg C (subparticle LLR-LRR)
Components
  • Envelope protein
  • Human antibody DENV-115 heavy chain
  • Human antibody DENV-115 light chain
  • Membrane protein
KeywordsVIRUS/IMMUNE SYSTEM / dengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex
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 / ribonucleoside triphosphate phosphatase activity / viral capsid / 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 / ribonucleoside triphosphate phosphatase activity / viral capsid / double-stranded RNA binding / channel activity / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / methyltransferase cap1 activity / mRNA 5'-cap (guanine-N7-)-methyltransferase activity / RNA helicase activity / protein dimerization activity / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / symbiont-mediated activation of host autophagy / serine-type endopeptidase activity / 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 / membrane
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 envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus envelope glycoprotein E, stem/anchor domain / : / Flavivirus NS3 helicase, C-terminal helical 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
Genome polyprotein / Polyprotein
Similarity search - Component
Biological speciesDengue virus type 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.4 Å
AuthorsFibriansah, G. / Ng, T.S. / Tan, A.W.K. / Shi, J. / Lok, S.M.
Funding support Singapore, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Singapore)NRF-NRFI2016-01 Singapore
CitationJournal: Nat Commun / Year: 2025
Title: Ultrapotent human antibodies lock E protein dimers central region of diverse DENV3 morphological variants.
Authors: Guntur Fibriansah / Thiam-Seng Ng / Xin-Ni Lim / Anastasia Shebanova / Lee Ching Ng / Song Ling Tan / Aaron W K Tan / Jian Shi / James E Crowe / Shee-Mei Lok /
Abstract: Dengue virus (DENV) consists of four serotypes (DENV1-4). Current vaccines induce differing levels of immune response against the four serotypes, that might prime recipients to develop severe disease ...Dengue virus (DENV) consists of four serotypes (DENV1-4). Current vaccines induce differing levels of immune response against the four serotypes, that might prime recipients to develop severe disease in subsequent infections. Several DENV tetravalent vaccine clinical trials suggested an increased incidence in severe DENV3 cases, suggesting a need to develop DENV3 therapeutics. Human monoclonal antibodies (HMAbs) DENV-290 and DENV-115 are ultrapotent against diverse DENV3 strains with differing particle morphologies. They mainly neutralize by inhibition of virus attachment to cells. CryoEM structures of Fabs complexed with differing DENV3 morphological variants show their Fabs binding across two E protein protomers at the center of the E dimer. This new class of E protein dimer binding antibodies is named EDE-C. The cryoEM structures also show how IgGs engage the DENV particles. Results define the structural and molecular basis for the ultrapotent activity of EDE-C antibodies.
History
DepositionJun 6, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Envelope protein
B: Membrane protein
C: Envelope protein
D: Membrane protein
E: Envelope protein
F: Membrane protein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain


Theoretical massNumber of molelcules
Total (without water)211,1958
Polymers211,1958
Non-polymers00
Water00
1
A: Envelope protein
B: Membrane protein
C: Envelope protein
D: Membrane protein
E: Envelope protein
F: Membrane protein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain

A: Envelope protein
B: Membrane protein
C: Envelope protein
D: Membrane protein
E: Envelope protein
F: Membrane protein
H: Human antibody DENV-115 heavy chain
L: Human antibody DENV-115 light chain


Theoretical massNumber of molelcules
Total (without water)422,39016
Polymers422,39016
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
2


  • Idetical with deposited unit
  • point asymmetric unit
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit in distinct coordinate
  • point asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: C2 (2 fold cyclic))

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Components

#1: Protein Envelope protein / Genome polyprotein / Coordinate model: Cα atoms only


Mass: 53682.484 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: A9LIF4
#2: Protein Membrane protein / Polyprotein / Coordinate model: Cα atoms only


Mass: 8347.836 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dengue virus type 3 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: M1J7M3
#3: Antibody Human antibody DENV-115 heavy chain / Coordinate model: Cα atoms only


Mass: 13607.289 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
#4: Antibody Human antibody DENV-115 light chain / Coordinate model: Cα atoms only


Mass: 11496.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Dengue virus serotype 3 strain 863DK in complex with human antibody DENV-115 Fab at 37 deg CCOMPLEXall0MULTIPLE SOURCES
2Dengue virus serotype 3 strain 863DKCOMPLEX#1-#21RECOMBINANT
3Human antibody DENV-115 Fab (heavy and light chain)COMPLEX#3-#41RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
21NO
31NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
23Homo sapiens (human)9606
32Dengue virus type 311069
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
13Homo sapiens (human)9606
22Aedes albopictus (Asian tiger mosquito)7160
Details of virus
IDEntity assembly-IDEmptyEnvelopedIsolateType
11NOYESSTRAINVIRION
22
33
Buffer solutionpH: 8
Details: NTE buffer (12 mM Tris-HCl pH 8.0, 120 mM NaCl and 1 mM EDTA)
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Details: The purified virus was mixed with DENV-115 Fab at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min. The complex was further incubated at ...Details: The purified virus was mixed with DENV-115 Fab at a molar ratio of 1.5 Fab for every E-protein and then the mixture was incubated at 4 deg C for 30 min. The complex was further incubated at 37 deg C for 30 min, and then incubated at 4 deg C for another 2 h.
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 5000 nm / Nominal defocus min: 400 nm
Image recordingElectron dose: 18 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k)

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Processing

EM software
IDNameCategory
7UCSF Chimeramodel fitting
9PHENIXmodel refinement
11RELIONfinal Euler assignment
13RELION3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C2 (2 fold cyclic)
3D reconstructionResolution: 5.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28155 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13J6S

3j6s

13J6S1PDBexperimental model
25IFA

5ifa

15IFA2PDBexperimental model
36QB6

6qb6

16QB63PDBexperimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00430732
ELECTRON MICROSCOPYf_angle_d0.76341670
ELECTRON MICROSCOPYf_dihedral_angle_d6.9684464
ELECTRON MICROSCOPYf_chiral_restr0.0474922
ELECTRON MICROSCOPYf_plane_restr0.0055184

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