7BUD

Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 8.0


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

A Human Antibody Neutralizes Different Flaviviruses by Using Different Mechanisms.

Zhang, S.Loy, T.Ng, T.S.Lim, X.N.Chew, S.V.Tan, T.Y.Xu, M.Kostyuchenko, V.A.Tukijan, F.Shi, J.Fink, K.Lok, S.M.

(2020) Cell Rep 31: 107584-107584

  • DOI: https://doi.org/10.1016/j.celrep.2020.107584
  • Primary Citation of Related Structures:  
    7BU8, 7BUA, 7BUB, 7BUD, 7BUE, 7BUF

  • PubMed Abstract: 

    Human antibody SIgN-3C neutralizes dengue virus (DENV) and Zika virus (ZIKV) differently. DENV:SIgN-3C Fab and ZIKV:SIgN-3C Fab cryoelectron microscopy (cryo-EM) complex structures show Fabs crosslink E protein dimers at extracellular pH 8.0 condition and also when further incubated at acidic endosomal conditions (pH 8.0-6.5). We observe Fab binding to DENV (pH 8.0-5.0) prevents virus fusion, and the number of bound Fabs increase (from 120 to 180). For ZIKV, although there are already 180 copies of Fab at pH 8.0, virus structural changes at pH 5.0 are not inhibited. The immunoglobulin G (IgG):DENV structure at pH 8.0 shows both Fab arms bind to epitopes around the 2-fold vertex. On ZIKV, an additional Fab around the 5-fold vertex at pH 8.0 suggests one IgG arm would engage with an epitope, although the other may bind to other viruses, causing aggregation. For DENV2 at pH 5.0, a similar scenario would occur, suggesting DENV2:IgG complex would aggregate in the endosome. Hence, a single antibody employs different neutralization mechanisms against different flaviviruses.


  • Organizational Affiliation

    Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore 169857, Singapore; Centre for BioImaging Sciences, National University of Singapore, Singapore 117557, Singapore.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SIgN-3C Fab heavy chainA [auth G],
I [auth H]
132Homo sapiensMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SIgN-3C Fab light chainB [auth I],
J [auth L]
107Homo sapiensMutation(s): 0 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Dengue virus serotype 2 E proteinC [auth B],
E [auth A],
G [auth C]
495dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for E0WXJ2 (dengue virus type 2)
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Go to UniProtKB:  E0WXJ2
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UniProt GroupE0WXJ2
Glycosylation
Glycosylation Sites: 2
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Dengue virus serotype 2 M proteinD [auth E],
F [auth D],
H [auth F]
72dengue virus type 2Mutation(s): 0 
UniProt
Find proteins for E0WXJ2 (dengue virus type 2)
Explore E0WXJ2 
Go to UniProtKB:  E0WXJ2
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UniProt GroupE0WXJ2
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth J],
L [auth K],
M
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Singapore)SingaporeNRF-NRFI2016-01
National Research Foundation (NRF, Singapore)SingaporeNRF2016NRF-CRP001-063

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary