9G0B: Capsid protein VP1

Name: PDB 9G0B: Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius)
Published: 2024-07-31
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Rhinovirus A2 uncoating intermediate revealing the natural pocket factor (pH 5.8 and 4 degrees Celsius). Determined by electron microscopy at 3.2 Å resolution. Released 31 Jul 2024.

Method: Electron microscopy
Resolution: 3.2 Å
Organism: rhinovirus A2
Chains: 4
Atoms: 6,339
Mol. weight: 94.95 kDa
Ligands: DAO
Released: 31 Jul 2024

Explore 9G0B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9G0B contains 26 α-helices and 52 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 A: 8 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
β-strand	13	1	1
β-strand	17	1	2
β-strand	31-32	2	3
α-helix	34-36	3
α-helix	44-46	3
β-strand	53	1	2
β-strand	58	1	1
β-strand	63	1	4
α-helix	64-68	5
β-strand	72-80	9	5
β-strand	91-95	5	6
α-helix	102-108	7
β-strand	113-128	16	5
β-strand	137-143	7	6
α-helix	148-150	3
α-helix	156-159	4
β-strand	165-169	5	6
β-strand	176-179	4	5
β-strand	188-189	2	5
β-strand	194	1	7
β-strand	212-217	6	6
β-strand	226-242	17	5
α-helix	246-248	3
β-strand	254	1	8

Chain B: 9 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	9
β-strand	12-15	4	9
β-strand	22-23	2	10
α-helix	24-26	3
α-helix	42-43	2
β-strand	44	1	10
α-helix	47-49	3
β-strand	54-55	2	10
β-strand	59-61	3	11
β-strand	68-72	5	12
α-helix	81-88	8
β-strand	91-101	11	10
β-strand	108-118	11	12
β-strand	124	1	13
α-helix	135-137	3
β-strand	144-145	2	12
α-helix	157	1
β-strand	158	1	13
α-helix	159	1
α-helix	162-164	3
α-helix	174-176	3
β-strand	179-183	5	12
β-strand	189-194	6	10
β-strand	203	1	10
β-strand	208	1	7
β-strand	211-223	13	12
β-strand	230-232	3	11
β-strand	233-244	12	10

Chain C: 8 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-32	3
β-strand	39	1	5
β-strand	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
α-helix	66-68	3
β-strand	70-73	4	3
β-strand	81-86	6	14
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	15
β-strand	113-120	8	3
β-strand	126-134	9	14
α-helix	139-141	3
α-helix	144-148	5
β-strand	151-156	6	14
β-strand	162-167	6	3
β-strand	176-177	2	15
β-strand	187-197	11	14
β-strand	205-214	10	3
β-strand	219-223	5	15
β-strand	236	1	8

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Capsid protein VP1	A	protein	283	rhinovirus A2	P04936 (AlphaFold model)
Capsid protein VP2	B	protein	261	rhinovirus A2	P04936 (AlphaFold model)
Capsid protein VP3	C	protein	237	rhinovirus A2	P04936 (AlphaFold model)
Capsid protein VP4	D	protein	68	rhinovirus A2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9G0B_1 Capsid protein VP1 (chains A)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTA

Sequence of entity 2 (B), FASTA

>9G0B_2 Capsid protein VP2 (chains B)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (C), FASTA

>9G0B_3 Capsid protein VP3 (chains C)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Sequence of entity 4 (D), FASTA

>9G0B_4 Capsid protein VP4 (chains D)
GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASNGASKLEFTQDPSKFTDPVKDVL
EKGIPTLQ

Ligands and cofactors

ID	Name	Formula	Copies
DAO	Lauric acid	C12 H24 O2	1

Primary citation

New rhinovirus uncoating intermediate reveals how sodium versus potassium ions influence RNA release. Real-Hohn, A., Blaas, D. Sci Rep (2025) 15:36768-36768. DOI 10.1038/s41598-025-20627-0 · PubMed

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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