6SMG: Coxsackievirus A10

Name: PDB 6SMG: Structure of Coxsackievirus A10
Published: 2020-01-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of Coxsackievirus A10. Determined by electron microscopy at 3.5 Å resolution. Released 15 Jan 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Coxsackievirus A10
Chains: 4
Atoms: 6,411
Mol. weight: 94.9 kDa
Ligands: SPH
Released: 15 Jan 2020

Explore 6SMG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6SMG contains 28 α-helices and 57 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: 13 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	6-11	6
β-strand	24	1	1
β-strand	28	1	2
β-strand	32	1	3
β-strand	47-48	2	4
α-helix	50-52	3
α-helix	54-56	3
β-strand	69	1	3
β-strand	74	1	2
α-helix	76-78	3
β-strand	79	1	5
α-helix	80-84	5
β-strand	88-96	9	6
β-strand	105-109	5	7
α-helix	112-114	3
α-helix	116-122	7
β-strand	125-140	16	6
β-strand	149-155	7	7
β-strand	157	1	8
β-strand	159	1	8
α-helix	160-162	3
α-helix	168-171	4
β-strand	177-181	5	7
α-helix	186	1
β-strand	187-191	5	6
β-strand	200-201	2	6
β-strand	206	1	9
β-strand	231-236	6	7
β-strand	245-262	18	6
α-helix	264-266	3
α-helix	269-270	2
β-strand	278	1	10
α-helix	288-289	2
β-strand	290	1	11

Chain B: 5 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	12
β-strand	21-25	5	12
β-strand	32-33	2	13
α-helix	34-36	3
β-strand	54	1	13
β-strand	64-71	8	13
β-strand	78-82	5	14
α-helix	90-98	9
β-strand	99-111	13	13
β-strand	119-128	10	14
β-strand	135	1	10
α-helix	149-152	4
β-strand	159-160	2	14
α-helix	164-166	3
α-helix	174-178	5
β-strand	181-185	5	14
β-strand	191-196	6	13
β-strand	205	1	13
β-strand	210	1	9
β-strand	213-224	12	14
β-strand	233-249	17	13

Chain C: 8 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	6
α-helix	31-33	3
β-strand	39-40	2	6
β-strand	42	1	5
α-helix	44-47	4
β-strand	51-52	2	4
β-strand	58	1	11
α-helix	63-67	5
β-strand	69-72	4	4
β-strand	80-85	6	15
α-helix	93-95	3
α-helix	98-102	5
β-strand	106	1	16
β-strand	108-110	3	17
β-strand	113-119	7	4
β-strand	126-134	9	15
α-helix	144-147	4
β-strand	151-156	6	15
β-strand	162-167	6	4
β-strand	176-177	2	17
α-helix	182-187	6
β-strand	191-201	11	15
β-strand	209-218	10	4
β-strand	223-224	2	17
β-strand	227	1	16

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	48	1	1
α-helix	50-52	3
β-strand	57	1	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	298	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Capsid protein VP2	B	protein	255	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Capsid protein VP3	C	protein	240	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Capsid protein VP4	D	protein	69	Coxsackievirus A10	Q6JKR9 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SMG_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALSSTVRRAITSGQDVNTAAGTAPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVMNRNGVLEATISHFFSRSGLVGVVNLTDGGTDTTGYAVWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTENGEARPFMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGQCPNNMMGTFAVRVVSRV
ASQLKLQTRVYMKLKHVRAWIPRPIRSQPYLLKNFPNYDSSKITYSARDRASIKQANM

Sequence of entity 2 (B), FASTA

>6SMG_2 Capsid protein VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVLAGRGSNTKPNEAPHPGFNTTFPGTAGASFNDPYVLDSGVPLSQSLIYP
HQWINLRTNNCATIIVPYINAVPFDSAINHSNFGLIVVPVSPLKYSSGATTAIPITVTIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>6SMG_3 Capsid protein VP3 (chains C)
GLPTELRPGTNQFLTTEDDTAAPILPGFSPTPSIHIPGEVRSLLELCRVETILEVNNTTD
ATGLNRLLIPVSAQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

Sequence of entity 4 (D), FASTA

>6SMG_4 Capsid protein VP4 (chains D)
MGAQVSSQRSGSHETGNVATGGSTINFTNINYYKDSYAASASRQDFTQDPKKFTQPVLDS
IRELSAPLN

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Hand-foot-and-mouth disease virus receptor KREMEN1 binds the canyon of Coxsackie Virus A10. Zhao, Y., Zhou, D., Ni, T. et al. Nat Commun (2020) 11:38-38. DOI 10.1038/s41467-019-13936-2 · PubMed

Other PDB entries of the same protein (UniProt Q6JKR9 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6SNW 3.9 Å, Structure of Coxsackievirus A10 complexed with its receptor KREMEN1
6SNB 4.4 Å, Structure of Coxsackievirus A10 A-particle

Browse structure collections

About this viewer

MolViewer shows 6SMG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.