9VFU: Mature CVA6 virus
Structure of mature CVA6 virus complexed with 1F4 Fab. Determined by electron microscopy at 2.11 Å resolution. Released 19 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 2.11 Å
- Organisms
- Coxsackievirus A6, Mus musculus
- Chains
- 6
- Atoms
- 7,728
- Mol. weight
- 120.16 kDa
- Ligands
- STE
- Released
- 19 Nov 2025
Explore 9VFU in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9VFU contains 41 α-helices and 83 β-strands across 6 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: 16 helices, 20 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 |
| α-helix | 29-30 | 2 | |
| β-strand | 43-44 | 2 | 3 |
| α-helix | 46-48 | 3 | |
| α-helix | 50-52 | 3 | |
| α-helix | 56-59 | 4 | |
| α-helix | 62-64 | 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 | 121-135 | 15 | 5 |
| β-strand | 145-151 | 7 | 7 |
| α-helix | 156-158 | 3 | |
| α-helix | 164-167 | 4 | |
| β-strand | 173-177 | 5 | 7 |
| α-helix | 182-183 | 2 | |
| β-strand | 184-187 | 4 | 5 |
| β-strand | 196-197 | 2 | 5 |
| β-strand | 202 | 1 | 8 |
| 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 | 32-33 | 2 | 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 | 82-86 | 5 | |
| 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 | 211 | 1 | 8 |
| β-strand | 214-225 | 12 | 14 |
| β-strand | 234-250 | 17 | 13 |
Chain C: 9 helices, 19 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 6-7 | 2 | |
| β-strand | 23 | 1 | 5 |
| α-helix | 30-33 | 4 | |
| 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 |
| β-strand | 61 | 1 | 15 |
| α-helix | 63-67 | 5 | |
| β-strand | 69-72 | 4 | 3 |
| β-strand | 80-85 | 6 | 16 |
| α-helix | 93-96 | 4 | |
| α-helix | 98-102 | 5 | |
| α-helix | 103-105 | 3 | |
| β-strand | 106-110 | 5 | 17 |
| β-strand | 113-119 | 7 | 3 |
| β-strand | 126 | 1 | 18 |
| β-strand | 128-134 | 7 | 16 |
| α-helix | 144-147 | 4 | |
| β-strand | 151-156 | 6 | 16 |
| β-strand | 162-167 | 6 | 3 |
| β-strand | 176-177 | 2 | 17 |
| α-helix | 182-187 | 6 | |
| β-strand | 191-196 | 6 | 16 |
| β-strand | 201 | 1 | 18 |
| β-strand | 209-218 | 10 | 3 |
| β-strand | 223-227 | 5 | 17 |
Chain D: 2 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-38 | 3 | |
| α-helix | 51-54 | 4 | |
| β-strand | 57 | 1 | 13 |
| β-strand | 68 | 1 | 11 |
Chain E: 1 helix, 12 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 3-6 | 4 | 19 |
| β-strand | 18-25 | 8 | 19 |
| α-helix | 29-31 | 3 | |
| β-strand | 32 | 1 | 15 |
| β-strand | 34-39 | 6 | 20 |
| β-strand | 45-51 | 7 | 20 |
| β-strand | 58-60 | 3 | 20 |
| β-strand | 68-73 | 6 | 19 |
| β-strand | 78-83 | 6 | 19 |
| β-strand | 93-97 | 5 | 20 |
| β-strand | 98 | 1 | 21 |
| β-strand | 104 | 1 | 21 |
| β-strand | 110 | 1 | 20 |
Chain F: 2 helices, 13 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 4-6 | 3 | 22 |
| β-strand | 10 | 1 | 23 |
| β-strand | 19-25 | 7 | 22 |
| β-strand | 33-38 | 6 | 23 |
| β-strand | 40 | 1 | 24 |
| β-strand | 42 | 1 | 24 |
| α-helix | 43-44 | 2 | |
| β-strand | 45-49 | 5 | 23 |
| β-strand | 53-54 | 2 | 23 |
| α-helix | 55 | 1 | |
| β-strand | 62-67 | 6 | 22 |
| β-strand | 70-75 | 6 | 22 |
| β-strand | 85-90 | 6 | 23 |
| β-strand | 98 | 1 | 23 |
| β-strand | 103 | 1 | 23 |
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 |
| Genome polyprotein | D | protein | 69 | Coxsackievirus A6 | E3VJS6 |
| VH | E | protein | 115 | Mus musculus | |
| VL | F | protein | 107 | Mus musculus | |
Sequence of entity 1 (A), FASTA
>9VFU_1 Genome polyprotein (chains A)
NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLI
ETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLEL
STYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSD
PPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGK
NIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPAS
PQRTS
Sequence of entity 2 (B), FASTA
>9VFU_2 Genome polyprotein (chains B)
SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSV
NRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQG
ALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIF
PHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTI
APLNSEFSGLRQAIKQ
Sequence of entity 3 (C), FASTA
>9VFU_3 Genome polyprotein (chains C)
GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTG
TTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKT
GGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ
Sequence of entity 4 (D), FASTA
>9VFU_4 Genome polyprotein (chains D)
MGAQVSTQKSGSHETRNVATEGSTINFTNINYYKDSYAASASRQDFAQDPAKFTRPVLDA
IREAAAPLQ
Sequence of entity 5 (E), FASTA
>9VFU_5 VH (chains E)
QVQLQQSGAELVKPGASVKLSCKASGYTFTSYYMYWVKQRPGQGLEWIGEINPSNGGTNF
NEKFKSKATLTVDKSSSTAYMQLSSLTSEDSAVYYCTRYGNYAYWGQGTLVTVSA
Sequence of entity 6 (F), FASTA
>9VFU_6 VL (chains F)
DIQMTQSPASLSVSVGETVTITCRASENIYSNLAWYQQKQGKSPQLLVYAATNLADGVPS
RFSGSGSGTQYSLKINSLQSEDFGSYYCQHFWGTPWTFGGGTKLEIK
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:
- 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
- 9VFP 3.33 Å, Structure of CVA6 empty particle
Browse structure collections
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