9VFR: Mature Coxsackievirus A6 virion
Structure of mature Coxsackievirus A6 virion complexed with its receptor KREMEN1. Determined by electron microscopy at 2.55 Å resolution. Released 19 Nov 2025.
- Method
- Electron microscopy
- Resolution
- 2.55 Å
- Organisms
- Coxsackievirus A6, Homo sapiens
- Chains
- 5
- Atoms
- 8,479
- Mol. weight
- 129.22 kDa
- Ligands
- NAG, MYR, STE
- Released
- 19 Nov 2025
Explore 9VFR in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9VFR contains 46 α-helices and 85 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: 16 helices, 20 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-16 | 5 | |
| α-helix | 20-23 | 4 | |
| β-strand | 24 | 1 | 1 |
| α-helix | 26-27 | 2 | |
| 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 | 56-58 | 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 | 121-135 | 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 | 181-183 | 3 | |
| 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 | 273-274 | 2 | 9 |
| α-helix | 278-280 | 3 | |
| β-strand | 285 | 1 | 10 |
Chain B: 11 helices, 20 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 | 28-33 | 6 | 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 | 134-135 | 2 | 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 | 228 | 1 | 15 |
| β-strand | 230 | 1 | 15 |
| β-strand | 234-240 | 7 | 13 |
| β-strand | 242-250 | 9 | 13 |
Chain C: 8 helices, 16 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23 | 1 | 5 |
| α-helix | 30-32 | 3 | |
| β-strand | 39 | 1 | 5 |
| β-strand | 42 | 1 | 4 |
| α-helix | 43-47 | 5 | |
| 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 | 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 | 126-134 | 9 | 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 | 191-201 | 11 | 16 |
| β-strand | 209-218 | 10 | 3 |
| β-strand | 223-227 | 5 | 17 |
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 |
Chain G: 8 helices, 27 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 46 | 1 | 18 |
| β-strand | 48 | 1 | 19 |
| β-strand | 54 | 1 | 18 |
| α-helix | 55-57 | 3 | |
| β-strand | 85 | 1 | 20 |
| β-strand | 94-96 | 3 | 20 |
| β-strand | 106-108 | 3 | 20 |
| β-strand | 110 | 1 | 19 |
| α-helix | 112-114 | 3 | |
| β-strand | 119-124 | 6 | 21 |
| β-strand | 136-138 | 3 | 21 |
| α-helix | 144-152 | 9 | |
| β-strand | 158-162 | 5 | 21 |
| β-strand | 166-170 | 5 | 21 |
| β-strand | 180-181 | 2 | 21 |
| α-helix | 183-186 | 4 | |
| β-strand | 187 | 1 | 22 |
| α-helix | 188 | 1 | |
| β-strand | 189 | 1 | 23 |
| α-helix | 190 | 1 | |
| β-strand | 197 | 1 | 23 |
| β-strand | 199 | 1 | 22 |
| β-strand | 200 | 1 | 21 |
| β-strand | 203-208 | 6 | 21 |
| β-strand | 216-218 | 3 | 24 |
| β-strand | 222-226 | 5 | 25 |
| α-helix | 233-235 | 3 | |
| β-strand | 239-245 | 7 | 24 |
| β-strand | 251-260 | 10 | 25 |
| β-strand | 268-271 | 4 | 24 |
| β-strand | 278-282 | 5 | 24 |
| α-helix | 284-286 | 3 | |
| β-strand | 294 | 1 | 25 |
| β-strand | 298-304 | 7 | 24 |
| β-strand | 313-321 | 9 | 25 |
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 |
| Kremen protein 1 | G | protein | 293 | Homo sapiens | Q96MU8 |
Sequence of entity 1 (A), FASTA
>9VFR_1 Genome polyprotein (chains A)
NDPITNAVESAVSALADTTISRVTAANTAASTHSLGTGRVPALQAAETGASSNSSDENLI
ETRCVMNRNGVNEASVEHFYSRAGLVGVVEVKDSGTSLDGYTVWPIDVMGFVQQRRKLEL
STYMRFDAEFTFVSNLNNSTTPGMLLQYMYVPPGAPKPDSRKSYQWQTATNPSVFAKLSD
PPPQVSVPFMSPATAYQWFYDGYPTFGEHKQATNLQYGQCPNNMMGHFAIRTVSESTTGK
NIHVRVYMRIKHVRAWVPRPLRSQAYMVKNYPTYSQTITNTATDRASITTTDYEGGVPAS
PQRTS
Sequence of entity 2 (B), FASTA
>9VFR_2 Genome polyprotein (chains B)
SPSVEACGYSDRVAQLTVGNSTITTQEAANIVLSYGEWPEYCPSTDATAVDKPTRPDVSV
NRFYTLSTKSWKTESTGWYWKFPDVLNDTGVFGQNAQFHYLYRSGFCMHVQCNASKFHQG
ALLVAAIPEFVIAASSPATKPNSQGLYPDFAHTNPGKDGQEFRDPYVLDAGIPLSQALIF
PHQWINLRTNNCATIIMPYINALPFDSALNHSNFGLVVIPISPLKYCNGATTEVPITLTI
APLNSEFSGLRQAIKQ
Sequence of entity 3 (C), FASTA
>9VFR_3 Genome polyprotein (chains C)
GFPTELKPGTNQFLTTDDGTSPPILPGFEPTPLIHIPGEFTSLLDLCQVETILEVNNTTG
TTGVSRLLIPVRAQNNVDQLCASFQVDPGRNGPWQSTMVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYTPPGSAQPTTREAAMLGTHIVWDFGLQSSVTLVIPWISNTHFRAVKT
GGVYDYYATGIVTIWYQTNFVVPPDTPTEANIIALGAAQKNFTLKLCKDTDEIQQTAEYQ
Sequence of entity 4 (D), FASTA
>9VFR_4 Genome polyprotein (chains D)
MGAQVSTQKSGSHETRNVATEGSTINFTNINYYKDSYAASASRQDFAQDPAKFTRPVLDA
IREAAAPLQ
Sequence of entity 5 (G), FASTA
>9VFR_5 Kremen protein 1 (chains G)
PECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGGLGEHNYCRNPDG
DVSPWCYVAEHEDGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSKTSNKLTIQTCIS
FCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQPCGGDGRIILFDT
LVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFPLFDIRDSADMVE
LLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVLYQAVK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| NAG | 2-acetamido-2-deoxy-beta-D-glucopyranose | C8 H15 N O6 | 2 |
| MYR | Myristic acid | C14 H28 O2 | 1 |
| 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
- 9VFQ 2.23 Å, Structure of mature CVA6 virus
- 9VFS 2.49 Å, Structure of Coxsackievirus A6 Altered-particles
- 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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