6SNW: Coxsackievirus A10

Name: PDB 6SNW: Structure of Coxsackievirus A10 complexed with its receptor KREMEN1
Published: 2020-01-15
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Structure of Coxsackievirus A10 complexed with its receptor KREMEN1. Determined by electron microscopy at 3.9 Å resolution. Released 15 Jan 2020.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Coxsackievirus A10, Homo sapiens
Chains: 5
Atoms: 8,720
Mol. weight: 137.13 kDa
Ligands: SPH, NAG
Released: 15 Jan 2020

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

Secondary structure: helices and β-sheets

6SNW contains 38 α-helices and 89 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: 14 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	5-12	8
β-strand	28	1	1
β-strand	32	1	2
β-strand	48	1	3
α-helix	50-52	3
α-helix	54-56	3
α-helix	60-62	3
β-strand	69	1	2
β-strand	74	1	1
α-helix	76-78	3
β-strand	79	1	4
α-helix	80-83	4
β-strand	88-92	5	5
β-strand	95-97	3	6
β-strand	105-109	5	7
α-helix	112-114	3
α-helix	116-122	7
β-strand	125-136	12	5
β-strand	140	1	6
β-strand	149-155	7	7
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	5
β-strand	200-201	2	5
β-strand	205	1	8
β-strand	231-236	6	7
β-strand	244-246	3	6
β-strand	249-262	14	5
α-helix	264-266	3
α-helix	269-270	2
α-helix	288-289	2
β-strand	290	1	9

Chain B: 9 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	15-16	2	10
β-strand	23-24	2	10
β-strand	32-33	2	11
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	12
β-strand	64-65	2	13
β-strand	69-71	3	14
β-strand	78-82	5	15
α-helix	90-96	7
β-strand	99-106	8	12
β-strand	107-111	5	11
β-strand	119	1	16
β-strand	121-128	8	15
α-helix	141-143	3
α-helix	149-152	4
β-strand	160	1	15
α-helix	164-166	3
α-helix	173-175	3
β-strand	181-185	5	15
β-strand	189	1	15
β-strand	191-195	5	11
β-strand	205	1	12
β-strand	211	1	8
β-strand	213-218	6	15
α-helix	222-223	2
β-strand	224	1	16
β-strand	233-235	3	14
β-strand	236-237	2	11
β-strand	238-239	2	13
β-strand	241-249	9	12

Chain C: 7 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	5
α-helix	30-32	3
β-strand	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
β-strand	58	1	9
α-helix	65-67	3
β-strand	68-72	5	3
β-strand	80-85	6	17
α-helix	93-95	3
α-helix	98-104	7
β-strand	106	1	18
β-strand	108-110	3	19
β-strand	113-119	7	3
β-strand	126-134	9	17
α-helix	144-147	4
β-strand	152-156	5	17
β-strand	162-167	6	3
β-strand	176-177	2	19
α-helix	184-187	4
β-strand	191-201	11	17
β-strand	209-218	10	3
β-strand	223-224	2	19
β-strand	227	1	18

Chain D: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	50-52	3
β-strand	57	1	11

Chain E: 7 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	55-57	3
β-strand	85	1	20
β-strand	94-96	3	20
β-strand	106-108	3	20
α-helix	109-110	2
β-strand	119-124	6	21
β-strand	136-138	3	21
α-helix	145-153	9
β-strand	158	1	22
β-strand	161-162	2	21
β-strand	166-168	3	21
β-strand	170	1	22
α-helix	175-177	3
β-strand	180	1	21
β-strand	187	1	23
α-helix	188	1
β-strand	189	1	24
α-helix	190	1
β-strand	197	1	24
β-strand	199	1	23
β-strand	200	1	21
β-strand	203-207	5	21
β-strand	208	1	22
β-strand	226	1	25
α-helix	233-234	2
β-strand	240-241	2	26
β-strand	244-245	2	26
β-strand	251-255	5	27
β-strand	258-260	3	25
β-strand	267-272	6	26
β-strand	278-283	6	26
β-strand	291-294	4	27
β-strand	298-304	7	26
β-strand	313-315	3	25
β-strand	319-321	3	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	298	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Coxsackievirus VP2	B	protein	255	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Capsid protein VP3	C	protein	240	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Coxsackievirus VP4	D	protein	69	Coxsackievirus A10	Q6JKR9 (AlphaFold model)
Kremen protein 1	E	protein	378	Homo sapiens	Q96MU8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6SNW_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALSSTVRRAITSGQDVNTAAGTAPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVMNRNGVLEATISHFFSRSGLVGVVNLTDGGTDTTGYAVWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTENGEARPFMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGQCPNNMMGTFAVRVVSRV
ASQLKLQTRVYMKLKHVRAWIPRPIRSQPYLLKNFPNYDSSKITYSARDRASIKQANM

Sequence of entity 2 (B), FASTA

>6SNW_2 Coxsackievirus VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVLAGRGSNTKPNEAPHPGFNTTFPGTAGASFNDPYVLDSGVPLSQSLIYP
HQWINLRTNNCATIIVPYINAVPFDSAINHSNFGLIVVPVSPLKYSSGATTAIPITVTIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>6SNW_3 Capsid protein VP3 (chains C)
GLPTELRPGTNQFLTTEDDTAAPILPGFSPTPSIHIPGEVRSLLELCRVETILEVNNTTD
ATGLNRLLIPVSAQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLIAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

Sequence of entity 4 (D), FASTA

>6SNW_4 Coxsackievirus VP4 (chains D)
MGAQVSSQRSGSHETGNVATGGSTINFTNINYYKDSYAASASRQDFTQDPKKFTQPVLDS
IRELSAPLN

Sequence of entity 5 (E), FASTA

>6SNW_5 Kremen protein 1 (chains E)
ETGAPSPGLGPGPECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGG
LGEHNYCRNPDGDVSPWCYVAEHEDGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSK
TSNKLTIQTCISFCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQP
CGGDGRIILFDTLVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFP
LFDIRDSADMVELLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVL
YQAVKEEGSENLYFQGGSLPQERPAVNQTVAEVITEQANLSVSAARSSKVLYVITTSPSH
PPQTVPGTHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	2

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
6SNB 4.4 Å, Structure of Coxsackievirus A10 A-particle

Browse structure collections

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