9VG1: CVA6 empty capsid

Name: PDB 9VG1: Structure of CVA6 empty capsid complexed with 3H7 Fab
Published: 2025-11-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of CVA6 empty capsid complexed with 3H7 Fab. Determined by electron microscopy at 3.26 Å resolution. Released 19 Nov 2025.

Method: Electron microscopy
Resolution: 3.26 Å
Organisms: Mus musculus, Coxsackievirus A6
Chains: 5
Atoms: 6,443
Mol. weight: 113.5 kDa
Released: 19 Nov 2025

Explore 9VG1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9VG1 contains 20 α-helices and 73 β-strands across 5 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: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	75	1	8
α-helix	76-79	4
β-strand	84-91	8	9
β-strand	101-105	5	10
α-helix	112-118	7
β-strand	121-135	15	9
β-strand	145-151	7	10
α-helix	156-158	3
α-helix	164-167	4
β-strand	173-177	5	10
α-helix	182-183	2
β-strand	184-187	4	9
β-strand	196-197	2	9
β-strand	202	1	11
α-helix	221-223	3
β-strand	227-232	6	10
β-strand	242-258	17	9
α-helix	260-262	3
β-strand	274-275	2	12
α-helix	283-284	2
β-strand	285	1	13

Chain B: 6 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	31-33	3	19
α-helix	34-36	3
α-helix	41-43	3
β-strand	54	1	20
β-strand	64-65	2	19
β-strand	69-71	3	19
β-strand	78-81	4	21
α-helix	90-97	8
β-strand	101-105	5	20
β-strand	106	1	22
β-strand	109-112	4	19
β-strand	119-128	10	21
β-strand	135-136	2	12
α-helix	150-153	4
α-helix	165-167	3
α-helix	174-179	6
β-strand	182-186	5	21
β-strand	192-196	5	19
β-strand	197	1	22
β-strand	206	1	20
β-strand	211	1	11
β-strand	214-225	12	21
β-strand	234-240	7	19
β-strand	243-248	6	20

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	9
α-helix	30-32	3
β-strand	39	1	9
β-strand	42	1	8
α-helix	44-47	4
β-strand	51-52	2	14
β-strand	58	1	13
α-helix	63-67	5
β-strand	69-72	4	14
β-strand	80-85	6	15
β-strand	88	1	16
β-strand	90	1	16
α-helix	93-96	4
α-helix	98-102	5
β-strand	108-111	4	17
β-strand	113-119	7	14
β-strand	126-127	2	18
β-strand	129-134	6	15
α-helix	144-147	4
β-strand	151-155	5	15
β-strand	162-166	5	14
β-strand	170-172	3	17
β-strand	191-195	5	15
β-strand	200-201	2	18
β-strand	209-218	10	14
β-strand	223-225	3	17

Chain D: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	5	1	1
β-strand	10-12	3	2
β-strand	20-24	5	1
β-strand	33-38	6	3
β-strand	44-49	6	3
β-strand	53-54	2	3
β-strand	64-65	2	1
β-strand	70-74	5	1
β-strand	85-90	6	3
β-strand	98	1	3
β-strand	103-105	3	2

Chain E: 0 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	4
β-strand	7	1	5
β-strand	21	1	5
β-strand	24-25	2	4
β-strand	34-39	6	6
β-strand	45-50	6	6
β-strand	70-72	3	7
β-strand	79-81	3	7
β-strand	93-98	6	6
β-strand	114	1	6
β-strand	118	1	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VL	D	protein	107	Mus musculus
VH	E	protein	124	Mus musculus
Genome polyprotein	A	protein	305	Coxsackievirus A6	A0A222NWY2
Genome polyprotein	C	protein	240	Coxsackievirus A6	A0A4P2SK07
Genome polyprotein	B	protein	256	Coxsackievirus A6	A0A7D0TR32

Sequence of entity 1 (D), FASTA

>9VG1_1 VL (chains D)
DIQMTQSPSSLSASLGERVSLTCRASQDIGSRLNWLQQEPDGTIKRLIYATSSLDSGVPK
RFSGSRSGSYYSLTISSLESEDFVDYYCLQYAGFPWTFGGGTKLEIK

Sequence of entity 2 (E), FASTA

>9VG1_2 VH (chains E)
EVKLVESGGGLVKPGGSLKLSCAASGFAFSTYDMSWVRQTPEKRLEWVATISSGGSYTYY
PDSVKGRFTISRDNARNTLYLQMSSLRSEDTALYYCARGGPYDYDGSFYTMDYWGQGTSV
TVSS

Sequence of entity 3 (A), FASTA

>9VG1_3 Genome polyprotein (chains A)
NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLI
ETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLEL
STYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSD
PPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGK
NIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPAS
PQRTS

Sequence of entity 4 (C), FASTA

>9VG1_4 Genome polyprotein (chains C)
GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTG
TTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKT
GGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ

Sequence of entity 5 (B), FASTA

>9VG1_5 Genome polyprotein (chains B)
SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSV
NRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQG
ALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIF
PHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTI
APLNSEFSGLRQAIKQ

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
9VFP 3.33 Å, Structure of CVA6 empty particle

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