7BZN: Mature Coxsackievirus A10 at pH 7.4

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

Cryo-EM structure of mature Coxsackievirus A10 at pH 7.4. Determined by electron microscopy at 3.1 Å resolution. Released 22 Jul 2020.

Method: Electron microscopy
Resolution: 3.1 Å
Organism: Coxsackievirus A10
Chains: 4
Atoms: 6,245
Mol. weight: 94.94 kDa
Ligands: SPH
Released: 22 Jul 2020

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

Secondary structure: helices and β-sheets

7BZN contains 27 α-helices and 60 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: 12 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	24-25	2	1
α-helix	30-32	3
β-strand	47-48	2	2
α-helix	50-52	3
α-helix	60-63	4
α-helix	76-78	3
β-strand	79	1	3
β-strand	88-95	8	4
β-strand	105-109	5	5
α-helix	116-122	7
β-strand	125-139	15	4
β-strand	149-155	7	5
α-helix	160-162	3
α-helix	169-171	3
β-strand	177-181	5	5
α-helix	185-186	2
β-strand	187-191	5	4
β-strand	200-201	2	4
β-strand	206	1	6
α-helix	225-227	3
β-strand	231-236	6	5
β-strand	246-262	17	4
α-helix	264-266	3
α-helix	269-270	2
β-strand	278	1	7
α-helix	283-285	3

Chain B: 7 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	8
β-strand	21-25	5	8
β-strand	32-33	2	9
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	10
β-strand	64-65	2	11
β-strand	69-70	2	12
β-strand	78-81	4	13
α-helix	90-98	9
β-strand	101-103	3	10
β-strand	106-107	2	9
β-strand	110-111	2	14
β-strand	119	1	15
β-strand	123-128	6	13
α-helix	131-134	4
β-strand	135	1	7
α-helix	149-152	4
β-strand	159-160	2	13
α-helix	164-166	3
β-strand	181-183	3	13
β-strand	191-192	2	14
β-strand	194-196	3	9
β-strand	205	1	10
β-strand	210	1	6
β-strand	213-218	6	13
β-strand	224	1	15
β-strand	234-235	2	12
β-strand	236-237	2	14
β-strand	238-239	2	11
β-strand	245-247	3	10

Chain C: 5 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	4
α-helix	31-33	3
β-strand	39-40	2	4
β-strand	42	1	3
β-strand	51-52	2	2
β-strand	68-72	5	2
β-strand	80-85	6	16
α-helix	93-96	4
α-helix	99-102	4
β-strand	106	1	17
β-strand	109-110	2	18
β-strand	113-120	8	2
β-strand	126-127	2	19
β-strand	128-134	7	16
α-helix	144-147	4
β-strand	151-156	6	16
β-strand	162-167	6	2
β-strand	176	1	18
α-helix	185-187	3
β-strand	191-195	5	16
β-strand	200-201	2	19
β-strand	209-218	10	2
β-strand	223-224	2	18
β-strand	227	1	17

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
β-strand	47-48	2	1
α-helix	50-52	3
β-strand	57	1	9
α-helix	60-62	3

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
Capsid protein VP4	D	protein	69	Coxsackievirus A10	G0YPI2

Sequence of entity 1 (A), FASTA

>7BZN_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALGSTARRAISSVTNAESAANTTPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVVNRNGVLETTINHFFSRSGLVGVVNLTDGGTDTTGYATWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTKNGEARPYMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGLCPNNMMGTFAVRVVSRE
ASQLKLQTRVYMKLKHVRAWVPRPIRSQPYLLKNFPNYDSSKITNSARDRSSIKQANM

Sequence of entity 2 (B), FASTA

>7BZN_2 Capsid protein VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVIAGRGSNTKPNEAPHPGFTTTFPGTTGATFHDPYVLDSGVPLSQALIYP
HQWINLRTNNCATVIVPYINAVPFDSAINHSNFGLIVIPVSPLKYSSGATTAIPITITIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>7BZN_3 Capsid protein VP3 (chains C)
GIPAELRPGTNQFLTTDDDTAAPILPGFTPTPTIHIPGEVHSLLELCRVETILEVNNTTE
ATGLTRLLIPVSSQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLVAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

Sequence of entity 4 (D), FASTA

>7BZN_4 Capsid protein VP4 (chains D)
MGAQVSTQKSGSHETGNVATGGSTINFTNINYYKDSYAASATRQDFTQDPKKFTQPVLDS
IRELSAPLN

Ligands and cofactors

ID	Name	Formula	Copies
SPH	Sphingosine	C18 H37 N O2	1

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
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
7C4Y 3.5 Å, Cryo-EM structure of empty Coxsackievirus A10 at pH 7.4
7C4T 3.6 Å, Cryo-EM structure of A particle Coxsackievirus A10 at pH 7.4

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