9VFP: CVA6 empty particle

Name: PDB 9VFP: Structure of CVA6 empty particle
Published: 2025-11-26
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of CVA6 empty particle. Determined by electron microscopy at 3.33 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 3.33 Å
Organism: Coxsackievirus A6
Chains: 3
Atoms: 4,880
Mol. weight: 88.03 kDa
Released: 26 Nov 2025

Explore 9VFP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VFP contains 20 α-helices and 50 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	75	1	1
α-helix	76-79	4
β-strand	84-91	8	2
β-strand	101-105	5	3
α-helix	112-118	7
β-strand	121-136	16	2
β-strand	145-151	7	3
α-helix	156-158	3
α-helix	164-167	4
β-strand	173-177	5	3
α-helix	182-183	2
β-strand	184-187	4	2
β-strand	196-197	2	2
β-strand	202	1	4
β-strand	227-232	6	3
β-strand	242-248	7	2
β-strand	250-258	9	2
α-helix	260-262	3
β-strand	268	1	5
β-strand	271	1	5
β-strand	274-275	2	6
β-strand	285	1	7

Chain B: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	8
α-helix	34-36	3
α-helix	41-43	3
β-strand	54	1	8
β-strand	64-65	2	8
α-helix	67-68	2
β-strand	69-71	3	8
β-strand	78-81	4	9
α-helix	83-86	4
α-helix	90-98	9
β-strand	101-112	12	8
β-strand	119-128	10	9
β-strand	135-136	2	6
α-helix	150-153	4
β-strand	160-161	2	9
α-helix	174-179	6
β-strand	182-186	5	9
β-strand	192-197	6	8
β-strand	206	1	8
β-strand	211	1	4
β-strand	214-225	12	9
β-strand	234-240	7	8
β-strand	242-248	7	8

Chain C: 7 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	2
α-helix	30-32	3
β-strand	39	1	2
β-strand	42	1	1
α-helix	43-47	5
β-strand	51-52	2	10
β-strand	58	1	7
α-helix	63-67	5
β-strand	69-72	4	10
β-strand	80-85	6	11
β-strand	88	1	12
β-strand	90	1	12
α-helix	93-96	4
α-helix	98-102	5
α-helix	103-105	3
β-strand	108-111	4	13
β-strand	113-119	7	10
β-strand	126-134	9	11
α-helix	144-148	5
β-strand	151-155	5	11
β-strand	162-166	5	10
β-strand	170-171	2	13
β-strand	191-201	11	11
β-strand	209-218	10	10
β-strand	223-225	3	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	305	Coxsackievirus A6	A0A222NWY2
Genome polyprotein	B	protein	256	Coxsackievirus A6	A0A7D0TR32
Genome polyprotein	C	protein	240	Coxsackievirus A6	A0A4P2SK07

Sequence of entity 1 (A), FASTA

>9VFP_1 Genome polyprotein (chains A)
NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLI
ETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLEL
STYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSD
PPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGK
NIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPAS
PQRTS

Sequence of entity 2 (B), FASTA

>9VFP_2 Genome polyprotein (chains B)
SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSV
NRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQG
ALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIF
PHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTI
APLNSEFSGLRQAIKQ

Sequence of entity 3 (C), FASTA

>9VFP_3 Genome polyprotein (chains C)
GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTG
TTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKT
GGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ

Primary citation

Molecular mechanisms of receptor recognition and antibody neutralization of coxsackievirus A6. Ke, X., Li, X., Liu, Z. et al. Nat Commun (2025) 17:934-934. DOI 10.1038/s41467-025-67666-9 · PubMed

Other PDB entries of the same protein (UniProt A0A222NWY2), best resolution first:

9VFU 2.11 Å, Structure of mature CVA6 virus complexed with 1F4 Fab
9VFQ 2.23 Å, Structure of mature CVA6 virus
9VFS 2.49 Å, Structure of Coxsackievirus A6 Altered-particles
9VFR 2.55 Å, Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1
9VFT 2.59 Å, Structure of mature CVA6 virus complexed with 3H7 Fab
9VG1 3.26 Å, Structure of CVA6 empty capsid complexed with 3H7 Fab

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