8AY5: Human rhinovirus 2 empty particle in situ

Name: PDB 8AY5: Human rhinovirus 2 empty particle in situ
Published: 2023-09-13
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Human rhinovirus 2 empty particle in situ. Determined by electron microscopy at 7.1 Å resolution. Released 13 Sept 2023.

Method: Electron microscopy
Resolution: 7.1 Å
Organism: rhinovirus A2
Chains: 3
Atoms: 5,823
Mol. weight: 82.86 kDa
Released: 13 Sept 2023

Explore 8AY5 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8AY5 contains 36 α-helices and 53 β-strands across 3 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, 17 β-strands

Element	Residues	Length	Sheet
β-strand	20-21	2	1
α-helix	23-25	3
α-helix	28-29	2
α-helix	33-35	3
α-helix	39-41	3
α-helix	49-51	3
β-strand	52	1	2
α-helix	53-56	4
β-strand	61-69	9	3
α-helix	75-78	4
β-strand	80-84	5	4
α-helix	91-97	7
β-strand	100-117	18	3
β-strand	126-132	7	4
α-helix	145-147	3
β-strand	154-158	5	4
α-helix	161-164	4
β-strand	165-168	4	3
β-strand	177-178	2	3
β-strand	183	1	5
β-strand	185	1	6
β-strand	189	1	6
α-helix	193-196	4
β-strand	201-206	6	4
β-strand	215-233	19	3
α-helix	235-236	2
β-strand	237	1	7
β-strand	243	1	8
β-strand	246	1	8

Chain B: 15 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	3-7	5	9
β-strand	10-14	5	9
α-helix	18-21	4
β-strand	22	1	10
α-helix	23-25	3
β-strand	43	1	10
α-helix	46-48	3
β-strand	53-54	2	10
α-helix	55-57	3
β-strand	58-60	3	11
β-strand	67-71	5	12
α-helix	73-75	3
α-helix	80-87	8
β-strand	88-100	13	10
β-strand	108-116	9	12
α-helix	121-122	2
β-strand	123	1	13
α-helix	133-136	4
α-helix	139-141	3
β-strand	143-144	2	12
α-helix	153-155	3
β-strand	157	1	13
α-helix	158	1
α-helix	161-163	3
β-strand	168	1	7
α-helix	173-175	3
β-strand	178-182	5	12
β-strand	188-193	6	10
β-strand	202	1	10
α-helix	204-206	3
β-strand	207	1	5
β-strand	210-221	12	12
β-strand	229-231	3	11
β-strand	232-245	14	10
α-helix	248-249	2

Chain C: 9 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	3
α-helix	30-32	3
β-strand	42	1	2
α-helix	44-48	5
β-strand	51-52	2	1
α-helix	65-68	4
β-strand	69-72	4	1
β-strand	81-86	6	14
α-helix	94-96	3
α-helix	98-104	7
β-strand	108-110	3	15
β-strand	113-119	7	1
β-strand	126	1	16
β-strand	128-134	7	14
α-helix	139-141	3
α-helix	144-149	6
β-strand	151-156	6	14
β-strand	162-167	6	1
β-strand	176-177	2	15
β-strand	187-192	6	14
α-helix	195-196	2
β-strand	197	1	16
α-helix	198-199	2
β-strand	206-214	9	1
β-strand	219-221	3	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	251	rhinovirus A2	P04936 (AlphaFold model)
Capsid protein VP2	B	protein	250	rhinovirus A2	P04936 (AlphaFold model)
VP3	C	protein	237	rhinovirus A2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8AY5_1 Capsid protein VP1 (chains A)
ALDAAETGHTSSVQPEDVIETRYVQTSQTRDEMSLESFLGRSGCIHESKLEVTLANYNKE
NFTVWAINLQEMAQIRRKFELFTYTRFDSEITLVPCISALSQDIGHITMQYMYVPPGAPV
PNSRDDYAWQSGTNASVFWQHGQAYPRFSLPFLSVASAYYMFYDGYDEQDQNYGTANTNN
MGSLCSRIVTEKHIHKVHIMTRIYHKAKHVKAWCPRPPRALEYTRAHRTNFKIEDRSIQT
AIVTRPIITTA

Sequence of entity 2 (B), FASTA

>8AY5_2 Capsid protein VP2 (chains B)
RIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSSNRFYTLRSVTW
SSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQGTLIVALIPEHQ
IASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTLLGNITIFPHQF
INLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTIPITISISPMCA
EFSGARAKRQ

Sequence of entity 3 (C), FASTA

>8AY5_3 VP3 (chains C)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Primary citation

Endosome rupture enables enteroviruses to infect cells. Ishemgulova, A. To be published.

Other PDB entries of the same protein (UniProt P04936 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5FX6 1.45 Å, Novel inhibitors of human rhinovirus 3C protease
5FX5 1.7 Å, Novel inhibitors of human rhinovirus 3C protease
6FFN 1.75 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
9W3O 1.76 Å, Crystal Structure of Human rhinovirus A2 3C Protease in Complex with a Broad-spectrum…
1CQQ 1.85 Å, Type 2 rhinovirus 3C protease with AG7088 inhibitor
6FFS 1.86 Å, Structure-based design and synthesis of macrocyclic human rhinovirus 3C protease…
2HRV 1.95 Å, 2A cysteine proteinase from human rhinovirus 2
1A3R 2.1 Å, FAB fragment (antibody 8F5) complexed with peptide from human rhinovirus (serotype 2)…
7ARA 2.24 Å, Rhinovirus A2 2A protease in complex with zVAM.fmk
2XYA 2.4 Å, Non-covalent inhibtors of rhinovirus 3C protease.
1FPN 2.6 Å, Human rhinovirus serotype 2 (HRV2)
3TN9 3.0 Å, X-ray structure of the HRV2 empty capsid (B-particle)

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