6SNB: Coxsackievirus A10 A-particle

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

Structure of Coxsackievirus A10 A-particle. Determined by electron microscopy at 4.4 Å resolution. Released 15 Jan 2020.

Method: Electron microscopy
Resolution: 4.4 Å
Organism: Coxsackievirus A10
Chains: 3
Atoms: 5,330
Mol. weight: 87.14 kDa
Released: 15 Jan 2020

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

Secondary structure: helices and β-sheets

6SNB contains 21 α-helices and 53 β-strands across 3 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, 17 β-strands

Element	Residues	Length	Sheet
α-helix	71-74	4
β-strand	79	1	1
α-helix	80-83	4
β-strand	88	1	2
β-strand	92-97	6	2
β-strand	105-109	5	3
β-strand	115	1	4
α-helix	118-123	6
β-strand	125	1	5
β-strand	127-128	2	6
β-strand	129-137	9	2
β-strand	140	1	2
β-strand	149-155	7	3
α-helix	160-162	3
α-helix	168-171	4
β-strand	177-181	5	3
α-helix	185-186	2
β-strand	187-191	5	2
β-strand	200-201	2	6
β-strand	231-236	6	3
β-strand	244-258	15	2
β-strand	260	1	7
β-strand	262	1	5
α-helix	264-266	3
α-helix	269-270	2

Chain B: 6 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	16-18	3	8
β-strand	21-23	3	8
β-strand	32-33	2	9
α-helix	34-36	3
α-helix	46-50	5
β-strand	54	1	9
β-strand	64-65	2	9
β-strand	69-71	3	9
β-strand	78-79	2	10
β-strand	82	1	10
α-helix	84-86	3
α-helix	90-96	7
β-strand	101-112	12	9
β-strand	119-128	10	10
α-helix	149-152	4
β-strand	160	1	10
α-helix	164-166	3
β-strand	181-185	5	10
β-strand	191-196	6	9
β-strand	205	1	9
β-strand	213-224	12	10
β-strand	233-247	15	9

Chain C: 7 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	2
α-helix	30-33	4
β-strand	39	1	7
β-strand	42	1	1
α-helix	44-47	4
β-strand	51-52	2	11
α-helix	64-67	4
β-strand	68-72	5	11
α-helix	76	1
β-strand	80-85	6	12
α-helix	98-104	7
β-strand	106	1	13
β-strand	109-110	2	14
β-strand	111-120	10	11
β-strand	126	1	15
β-strand	129-134	6	12
α-helix	139-141	3
α-helix	144-148	5
β-strand	152-155	4	12
β-strand	163	1	11
β-strand	166-170	5	11
β-strand	191-196	6	12
β-strand	201	1	15
β-strand	209-218	10	11
β-strand	223-224	2	14
β-strand	227	1	13
β-strand	237	1	4

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)

Sequence of entity 1 (A), FASTA

>6SNB_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALSSTVRRAITSGQDVNTAAGTAPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVMNRNGVLEATISHFFSRSGLVGVVNLTDGGTDTTGYAVWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTENGEARPFMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGQCPNNMMGTFAVRVVSRV
ASQLKLQTRVYMKLKHVRAWIPRPIRSQPYLLKNFPNYDSSKITYSARDRASIKQANM

Sequence of entity 2 (B), FASTA

>6SNB_2 Capsid protein VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVLAGRGSNTKPNEAPHPGFNTTFPGTAGASFNDPYVLDSGVPLSQSLIYP
HQWINLRTNNCATIIVPYINAVPFDSAINHSNFGLIVVPVSPLKYSSGATTAIPITVTIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>6SNB_3 Capsid protein VP3 (chains C)
GLPTELRPGTNQFLTTEDDTAAPILPGFSPTPSIHIPGEVRSLLELCRVETILEVNNTTD
ATGLNRLLIPVSAQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

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:

6SMG 3.5 Å, Structure of Coxsackievirus A10
6SNW 3.9 Å, Structure of Coxsackievirus A10 complexed with its receptor KREMEN1

Browse structure collections

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