7C2S

Helical reconstruction of Dengue virus serotype 3 complexed with Fab C10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

High flavivirus structural plasticity demonstrated by a non-spherical morphological variant.

Morrone, S.R.Chew, V.S.Y.Lim, X.N.Ng, T.S.Kostyuchenko, V.A.Zhang, S.Wirawan, M.Chew, P.L.Lee, J.Tan, J.L.Wang, J.Tan, T.Y.Shi, J.Screaton, G.Morais, M.C.Lok, S.M.

(2020) Nat Commun 11: 3112-3112

  • DOI: https://doi.org/10.1038/s41467-020-16925-y
  • Primary Citation of Related Structures:  
    7C2S, 7C2T

  • PubMed Abstract: 

    Previous flavivirus (dengue and Zika viruses) studies showed largely spherical particles either with smooth or bumpy surfaces. Here, we demonstrate flavivirus particles have high structural plasticity by the induction of a non-spherical morphology at elevated temperatures: the club-shaped particle (clubSP), which contains a cylindrical tail and a disc-like head. Complex formation of DENV and ZIKV with Fab C10 stabilize the viruses allowing cryoEM structural determination to ~10 Å resolution. The caterpillar-shaped (catSP) Fab C10:ZIKV complex shows Fabs locking the E protein raft structure containing three E dimers. However, compared to the original spherical structure, the rafts have rotated relative to each other. The helical tail structure of Fab C10:DENV3 clubSP showed although the Fab locked an E protein dimer, the dimers have shifted laterally. Morphological diversity, including clubSP and the previously identified bumpy and smooth-surfaced spherical particles, may help flavivirus survival and immune evasion.


  • Organizational Affiliation

    Program in Emerging Infectious Diseases, Duke-NUS Medical School, KTP Building, 8 College Road, Singapore, 169857, Singapore.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
envelope protein
A, B
394dengue virus type 3Mutation(s): 0 
UniProt
Find proteins for O39791 (dengue virus type 3)
Explore O39791 
Go to UniProtKB:  O39791
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO39791
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Heavy chain of Fab C10C [auth G],
E [auth I]
127Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
light chain of Fab C10D [auth H],
F [auth M]
109Homo sapiensMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 10.4 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report



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: 2020-07-08
    Type: Initial release
  • Version 1.1: 2021-01-13
    Changes: Other
  • Version 1.2: 2024-03-27
    Changes: Data collection, Database references, Derived calculations