7BUB | pdb_00007bub

Cryo-EM structure of Dengue virus serotype 2 complexed with Fab SIgN-3C at pH 6.5


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7BUB

This is version 2.2 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 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.

Macromolecule Content 

  • Total Structure Weight: 241.6 kDa 
  • Atom Count: 16,389 
  • Modeled Residue Count: 2,179 
  • Deposited Residue Count: 2,179 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
SIgN-3C Fab heavy chainA [auth G],
I [auth H]
132Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
SIgN-3C Fab light chainB [auth I],
J [auth L]
107Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Dengue virus serotype2 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)
Explore E0WXJ2 
Go to UniProtKB:  E0WXJ2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WXJ2
Glycosylation
Glycosylation Sites: 2
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
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
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE0WXJ2
Sequence Annotations
Expand
Reference Sequence

Oligosaccharides

Help  
Entity ID: 5
MoleculeChains Length2D Diagram GlycosylationD 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: 4.20 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2024-10-23
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 2.2: 2025-07-02
    Changes: Data collection