7BZT: Mature Coxsackievirus A10

Name: PDB 7BZT: Cryo-EM structure of mature Coxsackievirus A10 in complex with KRM1 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 in complex with KRM1 at pH 7.4. Determined by electron microscopy at 3.0 Å resolution. Released 22 Jul 2020.

Method: Electron microscopy
Resolution: 3.0 Å
Organisms: Coxsackievirus A10, Homo sapiens
Chains: 5
Atoms: 8,586
Mol. weight: 137.1 kDa
Ligands: NAG, SPH
Released: 22 Jul 2020

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

Secondary structure: helices and β-sheets

7BZT contains 31 α-helices and 82 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: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	28	1	1
β-strand	32	1	2
α-helix	54-56	3
β-strand	69	1	2
β-strand	74	1	1
β-strand	79	1	3
α-helix	80-83	4
β-strand	89-95	7	4
β-strand	108-109	2	5
α-helix	116-122	7
β-strand	125-131	7	6
β-strand	132	1	7
β-strand	135-140	6	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	187-188	2	4
β-strand	189-190	2	8
β-strand	191	1	7
β-strand	200-201	2	6
β-strand	206	1	9
α-helix	225-227	3
β-strand	231-236	6	5
β-strand	246-251	6	4
β-strand	255-262	8	6
α-helix	264-266	3
β-strand	278	1	10
α-helix	283-285	3

Chain B: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	11
β-strand	21-24	4	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
β-strand	64-65	2	12
β-strand	69-70	2	14
β-strand	78-79	2	15
α-helix	82-85	4
α-helix	90-98	9
β-strand	99-103	5	13
β-strand	106-111	6	12
β-strand	119-128	10	15
β-strand	135	1	10
α-helix	149-152	4
β-strand	159-160	2	15
α-helix	164-166	3
α-helix	174-178	5
β-strand	181-185	5	15
β-strand	191-196	6	12
β-strand	210	1	9
β-strand	213-224	12	15
β-strand	234-235	2	14
β-strand	236-240	5	12
β-strand	245-249	5	13

Chain C: 7 helices, 15 β-strands

Element	Residues	Length	Sheet
β-strand	22-23	2	8
α-helix	31-33	3
β-strand	39-40	2	6
β-strand	42	1	3
α-helix	44-47	4
β-strand	51-52	2	16
α-helix	64-66	3
β-strand	69-71	3	16
β-strand	80-85	6	17
α-helix	93-96	4
α-helix	98-105	8
β-strand	106-110	5	18
β-strand	113-119	7	16
β-strand	126-134	9	17
α-helix	144-147	4
β-strand	151-156	6	17
β-strand	162-167	6	16
β-strand	176-177	2	18
α-helix	182-187	6
β-strand	191-201	11	17
β-strand	210-218	9	16
β-strand	223-227	5	18

Chain D: 2 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	44-45	2
α-helix	51-54	4
β-strand	57	1	12

Chain E: 5 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	46	1	19
β-strand	54	1	19
β-strand	55-56	2	20
α-helix	57	1
β-strand	85	1	20
β-strand	94-97	4	20
α-helix	98-99	2
β-strand	106-108	3	20
β-strand	119-124	6	21
α-helix	144-152	9
β-strand	158-162	5	21
β-strand	170	1	21
β-strand	180	1	21
α-helix	181-182	2
β-strand	189	1	22
β-strand	197	1	22
β-strand	200	1	21
β-strand	203-208	6	21
β-strand	216-218	3	23
β-strand	224-226	3	24
α-helix	227	1
β-strand	239-244	6	23
β-strand	251-254	4	25
β-strand	259	1	26
β-strand	267-272	6	23
β-strand	277-283	7	23
β-strand	293-294	2	25
β-strand	299-304	6	23
β-strand	314	1	26
β-strand	315-317	3	24
β-strand	318-321	4	25

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
KRM1	E	protein	375	Homo sapiens	Q96MU8 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7BZT_1 Capsid protein VP1 (chains A)
GDPVEDIIHDALGSTARRAISSVTNAESAANTTPSSHRLETGRVPALQAAETGATSNATD
ENMIETRCVVNRNGVLETTINHFFSRSGLVGVVNLTDGGTDTTGYATWDIDIMGFVQLRR
KCEMFTYMRFNAEFTFVTTTKNGEARPYMLQYMYVPPGAPKPTGRDAFQWQTATNPSVFV
KLTDPPAQVSVPFMSPASAYQWFYDGYPTFGQHPETSNTTYGLCPNNMMGTFAVRVVSRE
ASQLKLQTRVYMKLKHVRAWVPRPIRSQPYLLKNFPNYDSSKITNSARDRSSIKQANM

Sequence of entity 2 (B), FASTA

>7BZT_2 Capsid protein VP2 (chains B)
SPSVEACGYSDRVAQLTVGNSSITTQEAANIVLAYGEWPEYCPDTDATAVDKPTRPDVSV
NRFYTLDSKMWQENSTGWYWKFPDVLNKTGVFGQNAQFHYLYRSGFCLHVQCNASKFHQG
ALLVAVIPEFVIAGRGSNTKPNEAPHPGFTTTFPGTTGATFHDPYVLDSGVPLSQALIYP
HQWINLRTNNCATVIVPYINAVPFDSAINHSNFGLIVIPVSPLKYSSGATTAIPITITIA
PLNSEFGGLRQAVSQ

Sequence of entity 3 (C), FASTA

>7BZT_3 Capsid protein VP3 (chains C)
GIPAELRPGTNQFLTTDDDTAAPILPGFTPTPTIHIPGEVHSLLELCRVETILEVNNTTE
ATGLTRLLIPVSSQNKADELCAAFMVDPGRIGPWQSTLVGQICRYYTQWSGSLKVTFMFT
GSFMATGKMLVAYSPPGSAQPANRETAMLGTHVIWDFGLQSSVSLVIPWISNTHFRTAKT
GGNYDYYTAGVVTLWYQTNYVVPPETPGEAYIIAMGAAQDNFTLKICKDTDEVTQQAVLQ

Sequence of entity 4 (D), FASTA

>7BZT_4 Capsid protein VP4 (chains D)
MGAQVSTQKSGSHETGNVATGGSTINFTNINYYKDSYAASATRQDFTQDPKKFTQPVLDS
IRELSAPLN

Sequence of entity 5 (E), FASTA

>7BZT_5 KRM1 (chains E)
APSPGLGPGPECFTANGADYRGTQNWTALQGGKPCLFWNETFQHPYNTLKYPNGEGGLGE
HNYCRNPDGDVSPWCYVAEHEDGVYWKYCEIPACQMPGNLGCYKDHGNPPPLTGTSKTSN
KLTIQTCISFCRSQRFKFAGMESGYACFCGNNPDYWKYGEAASTECNSVCFGDHTQPCGG
DGRIILFDTLVGACGGNYSAMSSVVYSPDFPDTYATGRVCYWTIRVPGASHIHFSFPLFD
IRDSADMVELLDGYTHRVLARFHGRSRPPLSFNVSLDFVILYFFSDRINQAQGFAVLYQA
VKEEGSENLYFQGGSLPQERPAVNQTVAEVITEQANLSVSAARSSKVLYVITTSPSHPPQ
TVPGTHHHHHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	3
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
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
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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