9VFR | pdb_00009vfr

Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1

• PDB DOI: https://doi.org/10.2210/pdb9VFR/pdb
• EM Map EMD-65032: EMDB EMDataResource

• Classification: VIRUS
• Organism(s): Coxsackievirus A6, Homo sapiens
• Expression System: Homo sapiens
• 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: 2.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1

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 300-mer - A60B60C60D60E60 Pseudo Symmetry: Icosahedral - I  (Explore in 3D)
Pseudo Stoichiometry: Hetero 300-mer - A120B60C60D60 

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 129.22 kDa 
• Atom Count: 8,479 
• Modeled Residue Count: 1,119 
• Deposited Residue Count: 1,163 
• Unique protein chains: 5

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
Kremen protein 1	E [auth G]	293	Homo sapiens	Mutation(s): 0  Gene Names: KREMEN1, KREMEN, KRM1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96MU8 (Homo sapiens) Explore Q96MU8  Go to UniProtKB:  Q96MU8
PHAROS:  Q96MU8 GTEx:  ENSG00000183762
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q96MU8-1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STE (Subject of Investigation/LOI)	F [auth A]	STEARIC ACID C18 H36 O2 QIQXTHQIDYTFRH-UHFFFAOYSA-N
MYR (Subject of Investigation/LOI)	G [auth D]	MYRISTIC ACID C14 H28 O2 TUNFSRHWOTWDNC-UHFFFAOYSA-N
NAG (Subject of Investigation/LOI)	H [auth G], I [auth G]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 2.55 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC	4.5.3

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