8GSC | pdb_00008gsc

Echovirus3 A-particle in complex with 6D10 Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structural Basis for the Immunogenicity of the C-Terminus of VP1 of Echovirus 3 Revealed by the Binding of a Neutralizing Antibody.

Qi, S.Fu, W.Fan, J.Zhang, L.Zheng, B.Wang, K.Wang, X.Zhu, L.Li, X.Zhang, Y.

(2022) Viruses 14

  • DOI: https://doi.org/10.3390/v14112322
  • Primary Citation Related Structures: 
    8GSC, 8GSD, 8GSE, 8GSF

  • PubMed Abstract: 

    Echovirus 3 (E3), a serotype of human enterovirus B (HEV-B), causes severe diseases in infants. Here, we determined the structures of E3 with a monoclonal antibody (MAb) 6D10 by cryo-EM to comprehensively understand the specificities and the immunological characteristic of this serotype. The solved cryo-EM structures of the F-, A-, and E-particles of E3 bound with 6D10 revealed the structural features of the virus-antibody interface. Importantly, the structures of E-particles bound with 6D10 revealed for the first time the nature of the C-terminus of VP1 for HEV-Bs at the structural level. The highly immunogenic nature of this region in the E-particles provides new strategies for vaccine development for HEV-Bs.


  • Organizational Affiliation
    • CAS Key Laboratory of Infection and Immunity, National Laboratory of Macromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.

Macromolecule Content 

  • Total Structure Weight: 106.14 kDa 
  • Atom Count: 7,453 
  • Modeled Residue Count: 949 
  • Deposited Residue Count: 949 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
VP1A [auth 1]237Echovirus E3Mutation(s): 0 
UniProt
Find proteins for A0A060BKX4 (Echovirus E3)
Explore A0A060BKX4 
Go to UniProtKB:  A0A060BKX4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A060BKX4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
VP2B [auth 2]247Echovirus E3Mutation(s): 0 
UniProt
Find proteins for A0A0K0LDT3 (Echovirus E3)
Explore A0A0K0LDT3 
Go to UniProtKB:  A0A0K0LDT3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0LDT3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
VP3C [auth 3]234Echovirus E3Mutation(s): 0 
UniProt
Find proteins for A0A0K0LDT3 (Echovirus E3)
Explore A0A0K0LDT3 
Go to UniProtKB:  A0A0K0LDT3
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0K0LDT3
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Heavy chain of 6D10D [auth H]117Mus musculusMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Light chain of 6D10E [auth L]114Mus musculusMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 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
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2022-12-14
    Type: Initial release
  • Version 1.1: 2024-10-30
    Changes: Data collection, Structure summary
  • Version 1.2: 2025-05-28
    Changes: Data collection