4L3B: HRV2 A particle uncoating intermediate

Name: PDB 4L3B: X-ray structure of the HRV2 A particle uncoating intermediate
Published: 2013-11-27
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

X-ray structure of the HRV2 A particle uncoating intermediate. Determined by X-ray diffraction at 6.5 Å resolution. Released 27 Nov 2013.

Method: X-ray diffraction
Resolution: 6.5 Å
Organism: Human rhinovirus A2
Chains: 3
Atoms: 5,514
Mol. weight: 88.04 kDa
Released: 27 Nov 2013

Explore 4L3B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4L3B contains 22 α-helices and 43 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: 5 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	1066	1	1
α-helix	1067-1070	4
β-strand	1075-1083	9	2
β-strand	1098	1	3
α-helix	1105-1111	7
β-strand	1116-1129	14	2
β-strand	1141-1146	6	3
β-strand	1167-1171	5	3
β-strand	1173	1	4
β-strand	1175	1	4
α-helix	1176-1178	3
β-strand	1179-1181	3	2
β-strand	1191-1192	2	2
β-strand	1215-1219	5	3
β-strand	1230-1245	16	2
α-helix	1249-1250	2
β-strand	1251	1	5
α-helix	1274-1276	3

Chain B: 7 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	2040-2042	3
α-helix	2058-2060	3
β-strand	2064-2069	6	6
α-helix	2070-2072	3
β-strand	2078-2082	5	7
α-helix	2092-2098	7
β-strand	2102-2112	11	6
β-strand	2121-2126	6	7
α-helix	2144-2147	4
β-strand	2179	1	5
α-helix	2183-2186	4
β-strand	2189-2192	4	7
β-strand	2202-2204	3	6
β-strand	2213	1	6
β-strand	2221-2229	9	7
α-helix	2241	1
β-strand	2242-2253	12	6

Chain C: 10 helices, 20 β-strands

Element	Residues	Length	Sheet
α-helix	3021-3022	2
β-strand	3023	1	2
α-helix	3028-3033	6
β-strand	3039-3040	2	2
β-strand	3042	1	1
α-helix	3044-3048	5
α-helix	3050	1
β-strand	3051-3052	2	8
α-helix	3053	1
α-helix	3065-3067	3
α-helix	3070-3071	2
β-strand	3072	1	9
β-strand	3081-3086	6	10
α-helix	3098-3103	6
β-strand	3106	1	11
β-strand	3108-3109	2	12
β-strand	3111-3116	6	8
β-strand	3119	1	13
β-strand	3126	1	14
β-strand	3129-3134	6	10
α-helix	3139-3141	3
β-strand	3152-3155	4	10
α-helix	3161-3164	4
β-strand	3176-3177	2	12
β-strand	3187-3192	6	10
β-strand	3197	1	14
β-strand	3206	1	9
β-strand	3208	1	13
β-strand	3211-3218	8	8
β-strand	3223	1	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein VP1	A	protein	289	Human rhinovirus A2	P04936 (AlphaFold model)
Protein VP2	B	protein	261	Human rhinovirus A2	P04936 (AlphaFold model)
Protein VP3	C	protein	237	Human rhinovirus A2	P04936 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>4L3B_1 Protein VP1 (chains A)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTAGPSDMY

Sequence of entity 2 (B), FASTA

>4L3B_2 Protein VP2 (chains B)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (C), FASTA

>4L3B_3 Protein VP3 (chains C)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Primary citation

Uncoating of common cold virus is preceded by RNA switching as determined by X-ray and cryo-EM analyses of the subviral A-particle. Pickl-Herk, A., Luque, D., Vives-Adrian, L. et al. Proc Natl Acad Sci U S A (2013) 110:20063-20068. DOI 10.1073/pnas.1312128110 · 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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