4Q4W: Coxsackievirus A24v

Name: PDB 4Q4W: High-resolution crystal structure of Coxsackievirus A24v
Published: 2014-11-05
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

High-resolution crystal structure of Coxsackievirus A24v. Determined by X-ray diffraction at 1.4 Å resolution. Released 5 Nov 2014.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: Coxsackievirus A24
Chains: 4
Atoms: 7,487
Mol. weight: 98.81 kDa
Ligands: CA, HEZ
Released: 5 Nov 2014

Explore 4Q4W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q4W contains 43 α-helices and 63 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 1: 16 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	27-29	3
β-strand	30	1	1
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	275-276	2
β-strand	277	1	9
α-helix	297-298	2
β-strand	299	1	10

Chain 2: 14 helices, 23 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
β-strand	184	1	9
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 3: 9 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	10
α-helix	65-67	3
α-helix	69	1
β-strand	70-73	4	3
β-strand	82-85	4	17
α-helix	98-103	6
β-strand	106-110	5	18
β-strand	113-119	7	3
β-strand	126	1	19
β-strand	128-134	7	17
α-helix	139-141	3
α-helix	144-147	4
β-strand	151-156	6	17
α-helix	157	1
β-strand	162-167	6	3
β-strand	176-177	2	18
β-strand	188-193	6	17
β-strand	198	1	19
β-strand	206-215	10	3
β-strand	220-224	5	18

Chain 4: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	20
α-helix	8-10	3
β-strand	26-29	4	20
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
Coxsackievirus capsid protein VP1	1	protein	305	Coxsackievirus A24	V9VEF3
Coxsackievirus capsid protein VP2	2	protein	271	Coxsackievirus A24	V9VEF3
Coxsackievirus capsid protein VP3	3	protein	240	Coxsackievirus A24	V9VEF3
Coxsackievirus capsid protein VP4	4	protein	69	Coxsackievirus A24	V9VEF3

Sequence of entity 1 (1), FASTA

>4Q4W_1 Coxsackievirus capsid protein VP1 (chains 1)
GIEETIDTVITNALQLSQPKPQKQPTAQSTPLTSGVNSQEVPALTAVETGASGQAVPSDV
IETRHVVNYKTRSESTLESFFGRSACVTILEVENFNATTDADRKKQFTTWAITYTDTVQL
RRKLEFFTYSRFDLEMTFVITERYYASNTGHARNQVYQLMYIPPGAPRPTAWDDYTWQSS
SNPSVFYTYGSAPPRMSIPYVGIANAYSHFYDGFARVPLKDETVDSGDTYYGLVTINDFG
TLAVRVVNEYNPARITSKIRVYMKPKHVRCWCPRPPRAVPYRGEGVDFKQDSITPLTAVE
NINTF

Sequence of entity 2 (2), FASTA

>4Q4W_2 Coxsackievirus capsid protein VP2 (chains 2)
SPNVEACGYSDRVRQITLGNSTITTQEAANAVVAYGEWPSYLDDKEANPIDAPTEPDVSS
NRFYTLDSVQWKSTSRGWWWKLPDALKDMGMFGQNMYYHYLGRSGYTVHVQCNASKFHQG
ALGVFAIPEYVMACNTEAKTSYVSYVNANPGEKGGVFDNAYNPSAEASEGRKFAALDYLL
GCGVLAGNAFVYPHQIINLRTNNSATLVLPYVNSLAIDCMAKHNNWGLVILPLCKLDYAP
NSSTEIPITVTIAPMFTEFNGLRNITVPATQ

Sequence of entity 3 (3), FASTA

>4Q4W_3 Coxsackievirus capsid protein VP3 (chains 3)
GLPTMLTPGSSQFLTSDDFQSPCALPNFDVTPPIHIPGEVFNMMELAEIDSMIPMNSVTG
KANTMEMYPIPLDDKGSATPIFSISLSPASDKRLQYTMLGEILNYYTHWTGSLRFTFLFC
GSMMATGKILLSYSPPGAKPPTTRKDAMLGTHIIWDLGLQSSCTMLAPWISNTVYRRCIK
DDFTEGGYITCFYQTRIVVPSGTPTSMFMLAFVSACPDFSVRLLRDTNHISQRTLFARAQ

Sequence of entity 4 (4), FASTA

>4Q4W_4 Coxsackievirus capsid protein VP4 (chains 4)
MGAQVSSQKVGAHENTNVATGGSTVNYTTINYYKDSASNAASKLDFSQDPSKFTEPVKDI
MIKTAPALN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	4
HEZ	Hexane-1,6-diol	C6 H14 O2	3

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

Primary citation

A sialic Acid binding site in a human picornavirus. Zocher, G., Mistry, N., Frank, M. et al. PLoS Pathog (2014) 10:e1004401-e1004401. DOI 10.1371/journal.ppat.1004401 · PubMed

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

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…
6TSD 1.81 Å, Crystal structure of human coxsackievirus A24v in complex with pentavalent inhibitor…
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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