3TN9: HRV2 empty capsid

Name: PDB 3TN9: X-ray structure of the HRV2 empty capsid (B-particle)
Published: 2012-03-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

X-ray structure of the HRV2 empty capsid (B-particle). Determined by X-ray diffraction at 3.0 Å resolution. Released 28 Mar 2012.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Human rhinovirus 2
Chains: 3
Atoms: 5,516
Mol. weight: 88.04 kDa
Released: 28 Mar 2012

Explore 3TN9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3TN9 contains 30 α-helices and 47 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 1: 9 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	63-65	3
β-strand	66	1	1
α-helix	67-71	5
β-strand	75-83	9	2
β-strand	95-98	4	3
α-helix	105-111	7
β-strand	116-130	15	2
β-strand	140-146	7	3
α-helix	151-153	3
α-helix	159-162	4
β-strand	167-172	6	3
α-helix	176-178	3
β-strand	179-182	4	2
β-strand	191-192	2	2
β-strand	197	1	4
α-helix	209-211	3
β-strand	215-220	6	3
β-strand	230-245	16	2
α-helix	249-250	2
β-strand	251	1	5
α-helix	274-276	3

Chain 2: 11 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	6
β-strand	21-24	4	6
β-strand	32-33	2	7
α-helix	34-36	3
α-helix	37-39	3
α-helix	41-43	3
β-strand	64-65	2	7
α-helix	66-68	3
β-strand	69-71	3	7
β-strand	78-81	4	8
α-helix	84-86	3
α-helix	90-97	8
β-strand	99-112	14	7
β-strand	118-128	11	8
β-strand	134	1	9
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	8
β-strand	168	1	9
α-helix	169	1
α-helix	172-174	3
β-strand	179	1	5
α-helix	184-186	3
β-strand	189-193	5	8
β-strand	199-204	6	7
β-strand	213	1	7
β-strand	218	1	4
β-strand	221-233	13	8
β-strand	240-256	17	7

Chain 3: 10 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	2
α-helix	30-33	4
β-strand	39-40	2	2
β-strand	42	1	1
α-helix	44-47	4
β-strand	51-52	2	10
α-helix	65-68	4
β-strand	69-72	4	10
α-helix	73	1
β-strand	81-86	6	11
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	12
β-strand	113-120	8	10
β-strand	126	1	13
β-strand	128-134	7	11
α-helix	139-141	3
α-helix	144-149	6
β-strand	152-156	5	11
β-strand	162-167	6	10
α-helix	168	1
β-strand	176-177	2	12
β-strand	187-192	6	11
β-strand	197	1	13
β-strand	206-214	9	10
β-strand	219-223	5	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein VP1	1	protein	289	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP2	2	protein	261	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP3	3	protein	237	Human rhinovirus 2	P04936 (AlphaFold model)

Sequence of entity 1 (1), FASTA

>3TN9_1 Protein VP1 (chains 1)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTAGPSDMY

Sequence of entity 2 (2), FASTA

>3TN9_2 Protein VP2 (chains 2)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (3), FASTA

>3TN9_3 Protein VP3 (chains 3)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Primary citation

Insights into minor group rhinovirus uncoating: the X-ray structure of the HRV2 empty capsid. Garriga, D., Pickl-Herk, A., Luque, D. et al. PLoS Pathog (2012) 8:e1002473-e1002473. DOI 10.1371/journal.ppat.1002473 · 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)
3VDD 3.2 Å, Structure of HRV2 capsid complexed with antiviral compound BTA798

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