9VFU | pdb_00009vfu

Structure of mature CVA6 virus complexed with 1F4 Fab

• PDB DOI: https://doi.org/10.2210/pdb9VFU/pdb
• EM Map EMD-65038: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Coxsackievirus A6, Mus musculus
• Expression System: Mus musculus
• Mutation(s): No 


• Deposited: 2025-06-11 Released: 2025-11-19 
• 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: 2.11 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Structure of mature CVA6 virus complexed with 1F4 Fab

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

To be published.

Biological Assembly 1  

Global Symmetry: Icosahedral - I  (Explore in 3D)
Global Stoichiometry: Hetero 360-mer - A60B60C60D60E60F60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 360-mer - A120B120C60D60 

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: 120.16 kDa 
• Atom Count: 7,728 
• Modeled Residue Count: 1,036 
• Deposited Residue Count: 1,092 
• Unique protein chains: 6

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

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Genome polyprotein	D	69	Coxsackievirus A6	Mutation(s): 0
UniProt
Find proteins for E3VJS6 (Coxsackievirus A6) Explore E3VJS6  Go to UniProtKB:  E3VJS6

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
VH	E	115	Mus musculus	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
VL	F	107	Mus musculus	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE (Subject of Investigation/LOI)	G [auth A]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.11 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: 2025-11-19 
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: 2025-11-19
  Type: Initial release