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- PDB-8jn7: Cryo-EM structure of the big tail club shape particle of dengue v... -

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Basic information

Entry
Database: PDB / ID: 8jn7
TitleCryo-EM structure of the big tail club shape particle of dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg C
Components
  • Human antibody DENV-290 heavy chain
  • Human antibody DENV-290 light chain
  • Polyprotein (Fragment)
KeywordsVIRUS/IMMUNE SYSTEM / dengue virus / human antibody / dengue-antibody structure / virus / VIRUS-IMMUNE SYSTEM complex
Function / homology
Function and homology information


clathrin-dependent endocytosis of virus by host cell / protein dimerization activity / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / virion membrane / extracellular region / membrane
Similarity search - Function
Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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 ...Envelope glycoprotein M, flavivirus / Envelope glycoprotein M superfamily, flavivirus / Flavivirus envelope glycoprotein M / Flavivirus polyprotein propeptide / Flavivirus polyprotein propeptide superfamily / Flavivirus polyprotein propeptide / 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, immunoglobulin-like domain / Flavivirus glycoprotein central and dimerisation domain / Flavivirus glycoprotein, central and dimerisation domains / Flaviviral glycoprotein E, central domain, subdomain 1 / Flaviviral glycoprotein E, central domain, subdomain 2 / Flavivirus/Alphavirus glycoprotein, immunoglobulin-like domain superfamily / Flavivirus glycoprotein, central and dimerisation domain superfamily / Flaviviral glycoprotein E, dimerisation domain / Immunoglobulin E-set
Similarity search - Domain/homology
Biological speciesdengue virus type 3
Homo sapiens (human)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 11 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.J. / 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

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Assembly

Deposited unit
C: Polyprotein (Fragment)
E: Polyprotein (Fragment)
H: Human antibody DENV-290 heavy chain
L: Human antibody DENV-290 light chain


Theoretical massNumber of molelcules
Total (without water)133,3394
Polymers133,3394
Non-polymers00
Water00
1
C: Polyprotein (Fragment)
E: Polyprotein (Fragment)
H: Human antibody DENV-290 heavy chain
L: Human antibody DENV-290 light chain
x 49


Theoretical massNumber of molelcules
Total (without water)6,533,623196
Polymers6,533,623196
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation48
MethodUCSF CHIMERA

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Components

#1: Protein Polyprotein (Fragment) / Coordinate model: Cα atoms only


Mass: 53730.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) dengue virus type 3 / Production host: Aedes albopictus (Asian tiger mosquito) / References: UniProt: Q07019
#2: Antibody Human antibody DENV-290 heavy chain / Coordinate model: Cα atoms only


Mass: 13495.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): EXPI293F / Cell line (production host): EXPI293F / Production host: Homo sapiens (human)
#3: Antibody Human antibody DENV-290 light chain / Coordinate model: Cα atoms only


Mass: 12381.966 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): EXPI293F / 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: helical reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Dengue virus serotype 3 strain CH53489 in complex with human antibody DENV-290 Fab at 37 deg CCOMPLEXall0MULTIPLE SOURCES
2Dengue virus serotype 3 strain CH53489COMPLEX#11RECOMBINANT
3Human antibody DENV-290 Fab (heavy and light chain)COMPLEX#2-#31RECOMBINANT
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
12Aedes albopictus (Asian tiger mosquito)7160
23Homo sapiens (human)9606
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-290 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-290 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: 500 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
Helical symmertyAngular rotation/subunit: 128.09 ° / Axial rise/subunit: 10.7 Å / Axial symmetry: C1
3D reconstructionResolution: 11 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35641 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13J6S

3j6s

13J6S1PDBexperimental model
23ZTJ

3ztj

13ZTJ2PDBexperimental model
35CHN

5chn

15CHN3PDBexperimental model

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