7C4Y: Empty Coxsackievirus A10 at pH 7.4

Name: PDB 7C4Y: Cryo-EM structure of empty Coxsackievirus A10 at pH 7.4
Published: 2020-07-22
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Cryo-EM structure of empty Coxsackievirus A10 at pH 7.4. Determined by electron microscopy at 3.5 Å resolution. Released 22 Jul 2020.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Coxsackievirus A10
Chains: 3
Atoms: 4,998
Mol. weight: 87.18 kDa
Released: 22 Jul 2020

Explore 7C4Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7C4Y contains 23 α-helices and 45 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, 12 β-strands

Element	Residues	Length	Sheet
β-strand	79	1	1
α-helix	80-84	5
β-strand	88-94	7	2
β-strand	106	1	3
α-helix	116-122	7
β-strand	125-140	16	2
β-strand	149-155	7	3
α-helix	160-162	3
α-helix	168-170	3
β-strand	177-181	5	3
α-helix	185-186	2
β-strand	187-191	5	2
β-strand	200-201	2	2
β-strand	206	1	4
β-strand	231-236	6	3
β-strand	246-262	17	2
α-helix	264-266	3
α-helix	269-270	2
β-strand	278	1	5
α-helix	283-285	3

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	6
α-helix	34-36	3
β-strand	54	1	7
β-strand	64-65	2	6
α-helix	66-68	3
β-strand	69-71	3	8
β-strand	78-81	4	9
α-helix	82-84	3
α-helix	90-97	8
β-strand	101-103	3	7
β-strand	106-111	6	6
β-strand	119-128	10	9
α-helix	131-134	4
β-strand	135	1	5
α-helix	149-152	4
β-strand	159-160	2	9
α-helix	173-178	6
β-strand	181-185	5	9
β-strand	191-192	2	6
β-strand	194-196	3	6
β-strand	205	1	7
β-strand	210	1	4
β-strand	213-224	12	9
β-strand	233-235	3	8
β-strand	236-240	5	6
β-strand	245-247	3	7

Chain C: 8 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	22-23	2	2
α-helix	31-33	3
β-strand	39-40	2	2
β-strand	42	1	1
α-helix	43-45	3
β-strand	52	1	10
α-helix	64-67	4
β-strand	69-72	4	10
β-strand	79-85	7	11
α-helix	93-95	3
α-helix	99-102	4
β-strand	106-110	5	12
β-strand	113-120	8	10
β-strand	128-134	7	11
α-helix	144-148	5
β-strand	151-156	6	11
β-strand	164-167	4	10
α-helix	168	1
β-strand	191-196	6	11
β-strand	209-218	10	10
β-strand	223-227	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	298	Coxsackievirus A10	A0A0C5AWF6
Capsid protein VP2	B	protein	255	Coxsackievirus A10	G0YPI2
Capsid protein VP3	C	protein	240	Coxsackievirus A10	G0YPI2

Sequence of entity 1 (A), FASTA

>7C4Y_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALGSTARRAISSVTNAESAANTTPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVVNRNGVLETTINHFFSRSGLVGVVNLTDGGTDTTGYATWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTKNGEARPYMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGLCPNNMMGTFAVRVVSRE
ASQLKLQTRVYMKLKHVRAWVPRPIRSQPYLLKNFPNYDSSKITNSARDRSSIKQANM

Sequence of entity 2 (B), FASTA

>7C4Y_2 Capsid protein VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVIAGRGSNTKPNEAPHPGFTTTFPGTTGATFHDPYVLDSGVPLSQALIYP
HQWINLRTNNCATVIVPYINAVPFDSAINHSNFGLIVIPVSPLKYSSGATTAIPITITIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>7C4Y_3 Capsid protein VP3 (chains C)
GIPAELRPGTNQFLTTDDDTAAPILPGFTPTPTIHIPGEVHSLLELCRVETILEVNNTTE
ATGLTRLLIPVSSQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLVAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

Primary citation

Molecular basis of Coxsackievirus A10 entry using the two-in-one attachment and uncoating receptor KRM1. Cui, Y., Peng, R., Song, H. et al. Proc Natl Acad Sci U S A (2020) 117:18711-18718. DOI 10.1073/pnas.2005341117 · PubMed

Other PDB entries of the same protein (UniProt A0A0C5AWF6), 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
6AKS 3.0 Å, Cryo-EM structure of CVA10 mature virus
7BZT 3.0 Å, Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 7.4
7BZU 3.0 Å, Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 at pH 5.5
7BZN 3.1 Å, Cryo-EM structure of mature Coxsackievirus A10 at pH 7.4
7BZO 3.2 Å, Cryo-EM structure of mature Coxsackievirus A10 at pH 5.5
7C4Z 3.3 Å, Cryo-EM structure of empty Coxsackievirus A10 at pH 5.5
7C4W 3.4 Å, Cryo-EM structure of A particle Coxsackievirus A10 at pH 5.5
7C4T 3.6 Å, Cryo-EM structure of A particle Coxsackievirus A10 at pH 7.4

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