6AKS: CVA10 mature virus

Name: PDB 6AKS: Cryo-EM structure of CVA10 mature virus
Published: 2019-01-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of CVA10 mature virus. Determined by electron microscopy at 3.0 Å resolution. Released 16 Jan 2019.

Method: Electron microscopy
Resolution: 3.0 Å
Organism: Coxsackievirus A10
Chains: 4
Atoms: 6,414
Mol. weight: 94.93 kDa
Ligands: SPH
Released: 16 Jan 2019

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

Secondary structure: helices and β-sheets

6AKS contains 32 α-helices and 59 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: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	1
β-strand	28	1	2
β-strand	32	1	3
β-strand	35	1	4
β-strand	48	1	5
α-helix	50-52	3
α-helix	54-56	3
α-helix	60-63	4
β-strand	66	1	4
β-strand	69	1	3
β-strand	74	1	2
α-helix	76-78	3
β-strand	79	1	6
α-helix	80-84	5
β-strand	88-95	8	7
β-strand	105-109	5	8
α-helix	112-114	3
α-helix	116-122	7
β-strand	125-140	16	7
β-strand	149-155	7	8
α-helix	160-162	3
α-helix	168-171	4
β-strand	177-181	5	8
α-helix	185-186	2
β-strand	187-191	5	7
β-strand	200-201	2	7
β-strand	206	1	9
α-helix	212-214	3
α-helix	225-227	3
β-strand	231-236	6	8
β-strand	246-262	17	7
α-helix	264-266	3
α-helix	269-270	2
β-strand	278	1	10
α-helix	283-285	3

Chain B: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	11
β-strand	21-25	5	11
β-strand	32-33	2	12
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	13
α-helix	57-59	3
β-strand	64-65	2	12
α-helix	67-68	2
β-strand	69-71	3	14
β-strand	78-82	5	15
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-103	5	13
β-strand	106-111	6	12
β-strand	118-128	11	15
β-strand	135	1	10
α-helix	149-152	4
β-strand	159-160	2	15
α-helix	173-178	6
β-strand	181-185	5	15
β-strand	191-196	6	12
α-helix	197-198	2
β-strand	205	1	13
β-strand	210	1	9
β-strand	213-225	13	15
β-strand	233-235	3	14
β-strand	236-240	5	12
β-strand	245-249	5	13

Chain C: 6 helices, 17 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	7
α-helix	30-33	4
β-strand	39-40	2	7
β-strand	42	1	6
β-strand	51-52	2	5
α-helix	65-67	3
β-strand	68-72	5	5
β-strand	80-85	6	16
α-helix	93-96	4
α-helix	98-102	5
β-strand	106-110	5	17
β-strand	113-120	8	5
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	5
β-strand	176-177	2	17
α-helix	184-187	4
β-strand	191-196	6	16
β-strand	201	1	18
β-strand	209-218	10	5
β-strand	223-227	5	17

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	47-48	2	1
α-helix	51-54	4
β-strand	57	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	A	protein	297	Coxsackievirus A10	W0G0K3
VP2	B	protein	255	Coxsackievirus A10	A0A0C5AZ80
VP3	C	protein	240	Coxsackievirus A10	A0A0C5AWF6
VP4	D	protein	69	Coxsackievirus A10	Q75Q92

Sequence of entity 1 (A), FASTA

>6AKS_1 VP1 (chains A)
GDPVEDIIHDALGSTARRAISSATNVESAANTTPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVVNRNGVLETTINHFFSRSGLVGVVNLTDGGTDTTGYVTWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTKNGEARPYMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGLCPNNMMGTFAVRVVSRE
ASQLKLQTRVYMKLKHVRAWVPRPIRSQPYLLKNFPNYDSSKITNSARDRSSIKQAN

Sequence of entity 2 (B), FASTA

>6AKS_2 VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVIAGRGSNTKPNEAPHPGFTTTFPGTTGATFHDPYVLDSGVPLSQALIYP
HQWINLRTNNCATVIVPYINAVPFDSAINHSNFGLIVIPVSPLKYSSGATTAIPITITIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>6AKS_3 VP3 (chains C)
GIPAELRPGTNQFLTTDDDTAAPILPGFTPTPTIHIPGEVHSLLELCRVETILEVNNTTE
ATGLTRLLIPVSSQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLVAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGADLYKFTLKICKDTDEVTQQAVLQ

Sequence of entity 4 (D), FASTA

>6AKS_4 VP4 (chains D)
MGAQVSTQKSGSHETGNVATGGSTINFTNINYYKDSYAASATRQDFTQDPKKFTQPVLDS
IRELSAPLN

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

Primary citation

Structures of Coxsackievirus A10 unveil the molecular mechanisms of receptor binding and viral uncoating. Zhu, L., Sun, Y., Fan, J. et al. Nat Commun (2018) 9:4985-4985. DOI 10.1038/s41467-018-07531-0 · PubMed

Other PDB entries of the same protein (UniProt W0G0K3), best resolution first:

6AKU 2.7 Å, Cryo-EM structure of CVA10 empty particle
6AKT 2.8 Å, Cryo-EM structure of CVA10 A-particle

Browse structure collections

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