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 7C2T | pdb_00007c2t

Helical reconstruction of Zika virus complexed with Fab C10


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report

Validation slider image for 7C2T

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 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.

Macromolecule Content 

  • Total Structure Weight: 177.45 kDa 
  • Atom Count: 1,610 
  • Modeled Residue Count: 1,610 
  • Deposited Residue Count: 1,630 
  • Unique protein chains: 4

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
envelope proteinA [auth B],
E [auth N]
504Zika virusMutation(s): 0 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
M proteinB [auth E],
F [auth Q]
75Zika virusMutation(s): 0 
UniProt
Find proteins for A0A024B7W1 (Zika virus (isolate ZIKV/Human/French Polynesia/10087PF/2013))
Explore A0A024B7W1 
Go to UniProtKB:  A0A024B7W1
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A024B7W1
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain from Fab C10C [auth K],
G [auth V]
127Homo sapiensMutation(s): 0 
Entity Groups
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain from Fab C10D [auth L],
H [auth W]
109Homo sapiensMutation(s): 0 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 9.40 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

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: 2024-03-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2025-07-02
    Changes: Data collection, Structure summary