9VFP | pdb_00009vfp

Structure of CVA6 empty particle

• PDB DOI: https://doi.org/10.2210/pdb9VFP/pdb
• EM Map EMD-65030: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Coxsackievirus A6
• Mutation(s): No 


• Deposited: 2025-06-11 Released: 2025-11-26 
• Deposition Author(s): Ke, X., Li, X., Liu, Z., Liu, K., Yan, X., Shu, B., Zhang, C.
• Funding Organization(s): National Science Foundation (NSF, China)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Molecular mechanisms of receptor recognition and antibody neutralization of coxsackievirus A6.

Ke, X., Li, X., Liu, Z., Liu, K., Liu, W., Yan, X., Shu, B., Zhang, C.

(2025) Nat Commun 17: 934-934

• PubMed: 41413343 
• DOI: https://doi.org/10.1038/s41467-025-67666-9
• Primary Citation Related Structures: 
  9VFP, 9VFQ, 9VFR, 9VFS, 9VFT, 9VFU, 9VG1


• PubMed Abstract: 
  

  Coxsackievirus A6 (CVA6), a major cause of hand, foot, and mouth disease, lacks approved vaccines or drugs. KRM1 is its only known receptor, but its precise role remains unclear. This study investigates CVA6's entry mechanism and antibody neutralization. Cryo-EM shows CVA6 clinical strain HeB primarily exists as mature virions. KRM1 binding within the canyon triggers conversion to uncoating intermediate, defining KRM1 as an uncoating receptor for CVA6. However, KRM1 knockout reduces CVA6 infectivity without affecting attachment. Conversely, disrupting heparan sulfate proteoglycan (HSPG) impairs both viral attachment and infectivity, and CVA6 virions bind heparin directly. These results support a two-receptor entry model for CVA6: HSPG mediates viral attachment, while KRM1 induces uncoating. Additionally, we develop two CVA6-specific protective antibodies (1F4 and 3H7), targeting a new antigenic site near the three-fold axis of the viral capsid. These antibodies sterically block KRM1 binding and function post-attachment, consistent with KRM1's role. The findings elucidate CVA6 entry and offer a basis for antibody interventions.

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Organizational Affiliation: 
• State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China.
Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China.
State Key Laboratory of Virology and Biosafety, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, Hubei, China. [e-mail].
Shanghai Institute of Infectious Disease and Biosecurity, Fudan University, Shanghai, China. [e-mail].

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 180-mer - A60B60C60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Homo 180-mer - A180 

Biological assembly 1 assigned by authors and generated by UCSF CHIMERA 1.18_b42531. (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 88.03 kDa 
• Atom Count: 4,880 
• Modeled Residue Count: 640 
• Deposited Residue Count: 801 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	A	305	Coxsackievirus A6	Mutation(s): 0
UniProt
Find proteins for A0A222NWY2 (Coxsackievirus A6) Explore A0A222NWY2  Go to UniProtKB:  A0A222NWY2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	B	256	Coxsackievirus A6	Mutation(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 A0A7D0TR32 (Coxsackievirus A6) Explore A0A7D0TR32  Go to UniProtKB:  A0A7D0TR32

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	C	240	Coxsackievirus A6	Mutation(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 A0A4P2SK07 (Coxsackievirus A6) Explore A0A4P2SK07  Go to UniProtKB:  A0A4P2SK07

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.33 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-11-26 
Deposition Author(s): Ke, X., Li, X., Liu, Z., Liu, K., Yan, X., Shu, B., Zhang, C.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, China)	China	--

Revision History  

• Version 1.0: 2025-11-26
  Type: Initial release
  
• Version 1.1: 2026-06-10
  Changes: Data collection, Database references