6TSD: Human coxsackievirus A24v

Name: PDB 6TSD: Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752
Published: 2021-07-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor ME0752. Determined by X-ray diffraction at 1.81 Å resolution. Released 7 Jul 2021.

Method: X-ray diffraction
Resolution: 1.81 Å
Organism: Coxsackievirus A24
Chains: 4
Atoms: 7,493
Mol. weight: 99.43 kDa
Ligands: CA, HEZ, SIA, MG
Released: 7 Jul 2021

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

Secondary structure: helices and β-sheets

6TSD contains 45 α-helices and 62 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 111: 17 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	28-29	2
β-strand	30	1	1
α-helix	31-32	2
β-strand	33	1	2
β-strand	44-45	2	3
α-helix	47-49	3
α-helix	51-53	3
α-helix	57-59	3
β-strand	63	1	2
β-strand	66	1	1
α-helix	73-75	3
β-strand	76	1	4
α-helix	77-81	5
β-strand	85-94	10	5
α-helix	100-103	4
α-helix	104-106	3
β-strand	107-111	5	6
α-helix	119-124	6
β-strand	127-144	18	5
α-helix	153-155	3
β-strand	156-162	7	6
α-helix	167-169	3
α-helix	175-178	4
β-strand	184-188	5	6
β-strand	195-198	4	5
β-strand	207-208	2	5
β-strand	213	1	7
β-strand	219	1	8
α-helix	233-235	3
β-strand	241-246	6	6
α-helix	249-251	3
β-strand	255-273	19	5
α-helix	275-277	3
α-helix	297-298	2
β-strand	299	1	9
β-strand	303	1	10

Chain 222: 14 helices, 22 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	44-46	3
α-helix	52-53	2
β-strand	54	1	12
α-helix	57-59	3
β-strand	64-65	2	12
α-helix	66-68	3
β-strand	69-71	3	13
β-strand	78-82	5	14
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	12
β-strand	119-128	10	14
β-strand	134	1	15
α-helix	145-148	4
α-helix	151-153	3
β-strand	155-156	2	14
β-strand	158	1	16
α-helix	167-169	3
β-strand	173	1	15
β-strand	176	1	16
α-helix	177-179	3
α-helix	186-191	6
β-strand	194-198	5	14
β-strand	204-209	6	12
β-strand	218	1	12
β-strand	223	1	7
β-strand	226-237	12	14
β-strand	246-248	3	13
β-strand	249-262	14	12
α-helix	265-266	2
β-strand	268	1	8

Chain 333: 10 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-33	4
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	43-47	5
β-strand	51-52	2	3
β-strand	58	1	9
α-helix	65-67	3
α-helix	69	1
β-strand	70-73	4	3
β-strand	82-85	4	10
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	17
β-strand	113-119	7	3
β-strand	126	1	18
β-strand	128-134	7	10
α-helix	139-141	3
α-helix	144-147	4
β-strand	151-156	6	10
α-helix	157	1
β-strand	162-167	6	3
β-strand	176-177	2	17
β-strand	188-193	6	10
β-strand	198	1	18
β-strand	206-215	10	3
β-strand	220-224	5	17

Chain 444: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	19
α-helix	8-10	3
β-strand	26-29	4	19
α-helix	36-38	3
α-helix	41-44	4
α-helix	51-54	4
β-strand	57	1	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	111	protein	305	Coxsackievirus A24	V9VEF3
Capsid protein VP2	222	protein	271	Coxsackievirus A24	V9VEF3
Capsid protein VP3	333	protein	240	Coxsackievirus A24	V9VEF3
Capsid protein VP4	444	protein	69	Coxsackievirus A24	V9VEF3

Sequence of entity 1 (111), FASTA

>6TSD_1 Capsid protein VP1 (chains 111)
GIEETIDTVITNALQLSQPKPQKQPTAQSTPLTSGVNSQEVPALTAVETGASGQAVPSDV
IETRHVVNYKTRSESTLESFFGRSACVTILEVENFNATTDADRKKQFTTWAITYTDTVQL
RRKLEFFTYSRFDLEMTFVITERYYASNTGHARNQVYQLMYIPPGAPRPTAWDDYTWQSS
SNPSVFYTYGSAPPRMSIPYVGIANAYSHFYDGFARVPLKDETVDSGDTYYGLVTINDFG
TLAVRVVNEYNPARITSKIRVYMKPKHVRCWCPRPPRAVPYRGEGVDFKQDSITPLTAVE
NINTF

Sequence of entity 2 (222), FASTA

>6TSD_2 Capsid protein VP2 (chains 222)
SPNVEACGYSDRVRQITLGNSTITTQEAANAVVAYGEWPSYLDDKEANPIDAPTEPDVSS
NRFYTLDSVQWKSTSRGWWWKLPDALKDMGMFGQNMYYHYLGRSGYTVHVQCNASKFHQG
ALGVFAIPEYVMACNTEAKTSYVSYVNANPGEKGGVFDNAYNPSAEASEGRKFAALDYLL
GCGVLAGNAFVYPHQIINLRTNNSATLVLPYVNSLAIDCMAKHNNWGLVILPLCKLDYAP
NSSTEIPITVTIAPMFTEFNGLRNITVPATQ

Sequence of entity 3 (333), FASTA

>6TSD_3 Capsid protein VP3 (chains 333)
GLPTMLTPGSSQFLTSDDFQSPCALPNFDVTPPIHIPGEVFNMMELAEIDSMIPMNSVTG
KANTMEMYPIPLDDKGSATPIFSISLSPASDKRLQYTMLGEILNYYTHWTGSLRFTFLFC
GSMMATGKILLSYSPPGAKPPTTRKDAMLGTHIIWDLGLQSSCTMLAPWISNTVYRRCIK
DDFTEGGYITCFYQTRIVVPSGTPTSMFMLAFVSACPDFSVRLLRDTNHISQRTLFARAQ

Sequence of entity 4 (444), FASTA

>6TSD_4 Capsid protein VP4 (chains 444)
MGAQVSSQKVGAHENTNVATGGSTVNYTTINYYKDSASNAASKLDFSQDPSKFTEPVKDI
MIKTAPALN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	5
HEZ	Hexane-1,6-diol	C6 H14 O2	4
SIA	N-acetyl-alpha-neuraminic acid	C11 H19 N O9	1
MG	Magnesium ion	Mg	1

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Pentavalent Sialic Acid Conjugates Block Coxsackievirus A24 Variant and Human Adenovirus Type 37-Viruses That Cause Highly Contagious Eye Infections. Johansson, E., Caraballo, R., Mistry, N. et al. ACS Chem Biol (2020) 15:2683-2691. DOI 10.1021/acschembio.0c00446 · PubMed

Other PDB entries of the same protein (UniProt V9VEF3), best resolution first:

4Q4W 1.4 Å, High-resolution crystal structure of Coxsackievirus A24v
4Q4X 1.65 Å, Crystal structure of Coxsackievirus A24v soaked with 6'-Sialyllactose (6SL)
7QB5 1.73 Å, Coxsackievirus A24v (CVA24v) in complex with a dimeric C2-C9-linked sialic acid inhibitor
7OJ7 1.78 Å, Crystal structure of human coxsackievirus A24v in complex with a pentavalent…
4Q4Y 1.88 Å, Crystal structure of Coxsackievirus A24v soaked with Disialyllacto-N-tetraose (DSLNT)
4Q4V 2.9 Å, Crystal structure of Coxsackievirus A24v
6EIT 3.9 Å, Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1

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