9VFQ: Mature CVA6 virus

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

Structure of mature CVA6 virus. Determined by electron microscopy at 2.23 Å resolution. Released 26 Nov 2025.

Method: Electron microscopy
Resolution: 2.23 Å
Organism: Coxsackievirus A6
Chains: 4
Atoms: 6,270
Mol. weight: 95.82 kDa
Ligands: STE
Released: 26 Nov 2025

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

Secondary structure: helices and β-sheets

9VFQ contains 36 α-helices and 56 β-strands across 4 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: 14 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	12-16	5
β-strand	24	1	1
α-helix	25-27	3
β-strand	28	1	2
β-strand	43-44	2	3
α-helix	46-48	3
α-helix	50-52	3
α-helix	56-58	3
β-strand	65	1	2
β-strand	70	1	1
α-helix	72-74	3
β-strand	75	1	4
α-helix	76-80	5
β-strand	84-91	8	5
β-strand	93-94	2	6
β-strand	97-98	2	6
β-strand	101-105	5	7
α-helix	112-118	7
β-strand	121-136	16	5
β-strand	145-151	7	7
β-strand	153	1	8
β-strand	155	1	8
α-helix	156-158	3
α-helix	164-167	4
β-strand	173-177	5	7
α-helix	181-183	3
β-strand	184-187	4	5
β-strand	196-197	2	5
β-strand	227-232	6	7
β-strand	242-258	17	5
α-helix	260-262	3
α-helix	265-266	2
β-strand	273-275	3	9
α-helix	278-280	3
β-strand	285	1	10

Chain B: 11 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	10	1	11
β-strand	14-18	5	12
β-strand	21-25	5	12
β-strand	31-33	3	13
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	13
α-helix	57-60	4
β-strand	64-71	8	13
β-strand	78-81	4	14
α-helix	82-85	4
α-helix	90-98	9
β-strand	99-111	13	13
β-strand	119-128	10	14
α-helix	131-133	3
β-strand	134-136	3	9
α-helix	144-146	3
α-helix	150-153	4
β-strand	160-161	2	14
α-helix	165-167	3
α-helix	174-179	6
β-strand	182-186	5	14
β-strand	192-197	6	13
β-strand	206	1	13
β-strand	214-225	12	14
β-strand	234-240	7	13
β-strand	242-250	9	13

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
β-strand	58	1	10
α-helix	63-67	5
β-strand	69-72	4	3
β-strand	80-85	6	15
α-helix	93-96	4
α-helix	98-103	6
β-strand	106-110	5	16
β-strand	113-119	7	3
β-strand	126-134	9	15
α-helix	135	1
α-helix	144-147	4
β-strand	151-156	6	15
β-strand	162-167	6	3
β-strand	176-177	2	16
α-helix	182-187	6
β-strand	191-201	11	15
β-strand	209-218	10	3
β-strand	223-227	5	16

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	51-54	4
β-strand	57	1	13
α-helix	60-62	3
β-strand	68	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	A	protein	305	Coxsackievirus A6	A0A222NWY2
VP2	B	protein	256	Coxsackievirus A6	A0A7D0TR32
VP3	C	protein	240	Coxsackievirus A6	A0A4P2SK07
VP4	D	protein	69	Coxsackievirus A6	E3VJS6

Sequence of entity 1 (A), FASTA

>9VFQ_1 VP1 (chains A)
NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLI
ETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLEL
STYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSD
PPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGK
NIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPAS
PQRTS

Sequence of entity 2 (B), FASTA

>9VFQ_2 VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSV
NRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQG
ALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIF
PHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTI
APLNSEFSGLRQAIKQ

Sequence of entity 3 (C), FASTA

>9VFQ_3 VP3 (chains C)
GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTG
TTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKT
GGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ

Sequence of entity 4 (D), FASTA

>9VFQ_4 VP4 (chains D)
MGAQVSTQKSGSHETRNVATEGSTINFTNINYYKDSYAASASRQDFAQDPAKFTRPVLDA
IREAAAPLQ

Ligands and cofactors

ID	Name	Formula	Copies
STE	Stearic acid	C18 H36 O2	1

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
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
9VFP 3.33 Å, Structure of CVA6 empty particle

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