9T6Z | pdb_00009t6z

EV-A71 (genotype B5) empty particle in complex with 16-3-3C Fab


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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Literature

Structural and functional mapping of protective human monoclonal antibodies against enterovirus A71.

Zhou, D.Kotecha, A.Kelly, J.T.Huang, P.N.Chen, Y.Y.Walter, T.S.Duyvesteyn, H.M.E.Owens, R.J.Ho, S.Y.Lin, T.Y.Fry, E.E.Ren, J.Huang, K.A.Stuart, D.I.

(2026) Sci Adv 12: eaee8217-eaee8217

  • DOI: https://doi.org/10.1126/sciadv.aee8217
  • Primary Citation Related Structures: 
    9I3W, 9I3Z, 9I40, 9I41, 9I42, 9I43, 9I45, 9I4B, 9I4C, 9I4D, 9I4E, 9RIG, 9RIH, 9RII, 9RIJ, 9RIK, 9RIL, 9RIM, 9RIN, 9RIO, 9RIP, 9RIQ, 9RIR, 9T6Z

  • PubMed Abstract: 

    EV-A71 has been responsible for recent severe HFMD outbreaks. We report structures for 12 potently neutralizing human anti-EV-A71 monoclonal antibody Fabs, alone and complexed with virus. Most recognize the native antigenic state with epitopes that span interfaces, together covering 85% of the capsid surface. The majority (8 of 12) bind the canyon, while the others cluster around the icosahedral two- and threefold axes. Blocking SCARB2 receptor binding likely contributes to neutralization for all, and a subset induces empty particles. A predominant gene family (IGHV4-39) does not dictate a common binding pose. Long CDR-H3 loops are frequently key to binding, especially at the canyon, suggesting that antigenicity data based on antibodies with shorter CDR3s (e.g., murine) may be misleading. This dataset reveals neutralization mechanisms for recently circulating EV-A71 genotypes, which will inform immunotherapies. We demonstrate synergy in vitro between canyon binding and both two- and threefold binding antibodies to increase neutralization potency.


  • Organizational Affiliation
    • College of Life Sciences, Zhejiang University, Hangzhou, China.

Macromolecule Content 

  • Total Structure Weight: 130.16 kDa 
  • Atom Count: 8,668 
  • Modeled Residue Count: 1,132 
  • Deposited Residue Count: 1,196 
  • Unique protein chains: 5

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab light chainA [auth L]216Homo sapiensMutation(s): 0 
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Fab heavy chainB [auth H]238Homo sapiensMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyproteinC [auth A]246Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for A0A7U3Q6X6 (Human enterovirus 71)
Explore A0A7U3Q6X6 
Go to UniProtKB:  A0A7U3Q6X6
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A7U3Q6X6
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyproteinD [auth B]254Enterovirus A71Mutation(s): 0 
EC: 3.4.22.29 (PDB Primary Data), 3.6.1.15 (PDB Primary Data), 3.4.22.28 (PDB Primary Data), 2.7.7.48 (PDB Primary Data)
UniProt
Find proteins for A0A0D3QR49 (Human enterovirus 71)
Explore A0A0D3QR49 
Go to UniProtKB:  A0A0D3QR49
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D3QR49
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Genome polyproteinE [auth C]242Enterovirus A71Mutation(s): 0 
UniProt
Find proteins for A0A1P8LK22 (Human enterovirus 71)
Explore A0A1P8LK22 
Go to UniProtKB:  A0A1P8LK22
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A1P8LK22
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N00065X/1

Revision History  (Full details and data files)

  • Version 1.0: 2026-04-29
    Type: Initial release
  • Version 1.1: 2026-06-17
    Changes: Data collection, Database references