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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


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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / viral capsid / 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 / ribonucleoside triphosphate phosphatase activity / double-stranded RNA binding / channel activity / viral capsid / monoatomic ion transmembrane transport / clathrin-dependent endocytosis of virus by host cell / mRNA (nucleoside-2'-O-)-methyltransferase 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 / induction by virus of host autophagy / viral RNA genome replication / serine-type endopeptidase activity / RNA-dependent RNA polymerase activity / virus-mediated perturbation of host defense response / fusion of virus membrane with host endosome membrane / viral envelope / host cell nucleus / virion attachment to host cell / structural molecule activity / virion membrane / proteolysis / extracellular region / ATP binding / membrane / metal ion binding
Similarity search - Function
Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B ...Flavivirus capsid protein C superfamily / Flavivirus non-structural protein NS2B / Genome polyprotein, Flavivirus / : / mRNA cap 0/1 methyltransferase / mRNA cap 0 and cap 1 methyltransferase (EC 2.1.1.56 and EC 2.1.1.57) domain profile. / Flavivirus non-structural protein NS4A / Flavivirus non-structural protein NS2B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus capsid protein C / Flavivirus non-structural protein NS4B / Flavivirus non-structural protein NS4A / Flavivirus NS2B domain profile. / Flavivirus non-structural protein NS2A / Flavivirus non-structural protein NS2A / RNA-directed RNA polymerase, thumb domain, Flavivirus / Flavivirus RNA-directed RNA polymerase, thumb domain / Flavivirus NS3, petidase S7 / Peptidase S7, Flavivirus NS3 serine protease / Flavivirus NS3 protease (NS3pro) domain profile. / RNA-directed RNA polymerase, flavivirus / Flavivirus RNA-directed RNA polymerase, fingers and palm domains / Flavivirus non-structural Protein NS1 / Flavivirus non-structural protein NS1 / Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / Flavivirus envelope glycoprotein M / Flavivirus envelope glycoprotein E, stem/anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain / Flavivirus envelope glycoprotein E, Stem/Anchor domain superfamily / Flavivirus glycoprotein E, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / : / Flavivirus NS3 helicase, C-terminal helical domain / Flavivirus glycoprotein, immunoglobulin-like 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: To Be Published
Title: Ultrapotent human antibodies lock E protein dimers of diverse DENV3 morphological variants
Authors: Fibriansah, G. / Ng, T.S. / Lim, X.N. / Shebanova, A. / Ng, L.C. / Tan, S.L. / Tan, A.W.K. / Shi, J. / Crowe, J.E. / Lok, S.M.
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)

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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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