6EIT: Coxsackievirus A24v

Name: PDB 6EIT: Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1
Published: 2018-01-10
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Coxsackievirus A24v in complex with the D1-D2 fragment of ICAM-1. Determined by electron microscopy at 3.9 Å resolution. Released 10 Jan 2018.

Method: Electron microscopy
Resolution: 3.9 Å
Organisms: Coxsackievirus A24, Homo sapiens
Chains: 4
Atoms: 6,734
Mol. weight: 100.13 kDa
Released: 10 Jan 2018

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

Secondary structure: helices and β-sheets

6EIT contains 26 α-helices and 71 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: 12 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	30	1	1
β-strand	33	1	2
α-helix	47-49	3
α-helix	57-60	4
β-strand	63	1	2
β-strand	66	1	1
α-helix	77-80	4
β-strand	85-86	2	3
β-strand	90-94	5	4
β-strand	107-111	5	5
α-helix	120-124	5
β-strand	127-137	11	6
β-strand	138-144	7	4
β-strand	156-162	7	5
β-strand	164	1	7
β-strand	166	1	7
α-helix	167-169	3
α-helix	175-178	4
β-strand	184-188	5	5
α-helix	192-194	3
β-strand	195-198	4	6
β-strand	207-208	2	6
β-strand	213	1	8
β-strand	219	1	9
β-strand	229	1	10
α-helix	230-231	2
α-helix	232-235	4
β-strand	241-246	6	5
β-strand	255-261	7	4
β-strand	262-263	2	3
β-strand	264-273	10	6
α-helix	275-277	3
α-helix	280-281	2
α-helix	290-292	3

Chain 2: 8 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
β-strand	64-65	2	12
β-strand	69-71	3	13
β-strand	78-81	4	14
α-helix	82-85	4
α-helix	92-97	6
β-strand	99-111	13	12
β-strand	121-128	8	14
β-strand	134	1	15
β-strand	155-156	2	14
β-strand	158	1	16
β-strand	173	1	15
β-strand	176	1	16
α-helix	186-191	6
β-strand	195-198	4	14
β-strand	204-209	6	12
β-strand	218	1	12
β-strand	223	1	8
β-strand	226-232	7	14
β-strand	246-248	3	13
β-strand	249-262	14	12
α-helix	265-266	2
β-strand	268	1	9

Chain 3: 6 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	13-14	2	5
α-helix	30-33	4
α-helix	43-45	3
β-strand	51-52	2	17
β-strand	70-72	3	18
β-strand	83-85	3	19
α-helix	98-103	6
β-strand	108-110	3	20
β-strand	113-119	7	18
β-strand	126-134	9	19
α-helix	139-141	3
α-helix	144-147	4
β-strand	151-156	6	19
β-strand	162-167	6	18
β-strand	176-177	2	20
β-strand	188-198	11	19
β-strand	207-211	5	18
β-strand	212-213	2	17
β-strand	214-215	2	18
β-strand	220-222	3	20

Chain 4: 0 helices, 12 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	21
β-strand	8-10	3	22
β-strand	17-20	4	23
β-strand	21-23	3	21
β-strand	30	1	10
β-strand	31-34	4	24
β-strand	39	1	23
β-strand	42	1	23
β-strand	51-54	4	23
β-strand	64-67	4	24
β-strand	77	1	24
β-strand	79-81	3	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
VP1	1	protein	305	Coxsackievirus A24	V9VEF3
VP2	2	protein	271	Coxsackievirus A24	V9VEF3
VP3	3	protein	240	Coxsackievirus A24	V9VEF3
Intercellular adhesion molecule 1	4	protein	85	Homo sapiens	P05362 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>6EIT_1 VP1 (chains 1)
GIEETIDTVITNALQLSQPKPQKQPTAQSTPLTSGVNSQEVPALTAVETGASGQAVPSDV
IETRHVVNYKTRSESTLESFFGRSACVTILEVENFNATTDADRKKQFTTWAITYTDTVQL
RRKLEFFTYSRFDLEMTFVITERYYASNTGHARNQVYQLMYIPPGAPRPTAWDDYTWQSS
SNPSVFYTYGSAPPRMSIPYVGIANAYSHFYDGFARVPLKDETVDSGDTYYGLVTINDFG
TLAVRVVNEYNPARITSKIRVYMKPKHVRCWCPRPPRAVPYRGEGVDFKQDSITPLTAVE
NINTF

Sequence of entity 2 (2), FASTA

>6EIT_2 VP2 (chains 2)
SPNVEACGYSDRVRQITLGNSTITTQEAANAVVAYGEWPSYLDDKEANPIDAPTEPDVSS
NRFYTLDSVQWKSTSRGWWWKLPDALKDMGMFGQNMYYHYLGRSGYTVHVQCNASKFHQG
ALGVFAIPEYVMACNTEAKTSYVSYVNANPGEKGGVFDNAYNPSAEASEGRKFAALDYLL
GCGVLAGNAFVYPHQIINLRTNNSATLVLPYVNSLAIDCMAKHNNWGLVILPLCKLDYAP
NSSTEIPITVTIAPMFTEFNGLRNITVPATQ

Sequence of entity 3 (3), FASTA

>6EIT_3 VP3 (chains 3)
GLPTMLTPGSSQFLTSDDFQSPCALPNFDVTPPIHIPGEVFNMMELAEIDSMIPMNSVTG
KANTMEMYPIPLDDKGSATPIFSISLSPASDKRLQYTMLGEILNYYTHWTGSLRFTFLFC
GSMMATGKILLSYSPPGAKPPTTRKDAMLGTHIIWDLGLQSSCTMLAPWISNTVYRRCIK
DDFTEGGYITCFYQTRIVVPSGTPTSMFMLAFVSACPDFSVRLLRDTNHISQRTLFARAQ

Sequence of entity 4 (4), FASTA

>6EIT_4 Intercellular adhesion molecule 1 (chains 4)
QTSVSPSKVILPRGGSVLVTCSTSCDQPKLLGIETPLPKKELLLPGNNRKVYELSNVQED
SQPMCYSNCPDGQSTAKTFLTVYWT

Primary citation

Role of enhanced receptor engagement in the evolution of a pandemic acute hemorrhagic conjunctivitis virus. Baggen, J., Hurdiss, D.L., Zocher, G. et al. Proc Natl Acad Sci U S A (2018) 115:397-402. DOI 10.1073/pnas.1713284115 · 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…
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

Browse structure collections

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