3DPR: Human rhinovirus 2

Name: PDB 3DPR: Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3
Published: 2009-04-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

Human rhinovirus 2 bound to a concatamer of the VLDL receptor module V3. Determined by X-ray diffraction at 3.5 Å resolution. Released 7 Apr 2009.

Method: X-ray diffraction
Resolution: 3.5 Å
Organisms: Human rhinovirus 2, Homo sapiens
Chains: 5
Atoms: 6,450
Mol. weight: 99.91 kDa
Ligands: CA, DAO
Released: 7 Apr 2009

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

Secondary structure: helices and β-sheets

3DPR contains 28 α-helices and 63 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: 11 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	16	1	1
α-helix	17-18	2
β-strand	20	1	2
α-helix	41-43	3
α-helix	47-50	4
β-strand	56	1	2
β-strand	61	1	1
α-helix	63-65	3
β-strand	66	1	3
α-helix	67-71	5
β-strand	75-83	9	4
β-strand	90	1	5
β-strand	92	1	5
β-strand	94-98	5	6
α-helix	106-111	6
β-strand	114-126	13	4
β-strand	129-131	3	4
β-strand	140-146	7	6
β-strand	148	1	7
β-strand	150	1	7
α-helix	151-153	3
α-helix	159-162	4
β-strand	167-172	6	6
β-strand	179-182	4	4
β-strand	191-192	2	4
β-strand	197	1	8
α-helix	207-209	3
β-strand	215-220	6	6
β-strand	229-247	19	4
α-helix	249-251	3
β-strand	257	1	9
α-helix	274-276	3
β-strand	277	1	10

Chain B: 10 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	15-18	4	11
β-strand	21-24	4	11
β-strand	32-33	2	12
α-helix	34-36	3
β-strand	54	1	12
α-helix	57-59	3
β-strand	64-65	2	12
β-strand	69-72	4	13
β-strand	78-80	3	14
α-helix	85-87	3
α-helix	90-98	9
β-strand	99-111	13	12
β-strand	118-126	9	14
β-strand	134	1	15
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	14
α-helix	164-166	3
α-helix	167	1
β-strand	168	1	15
α-helix	169	1
α-helix	172-174	3
β-strand	189-192	4	14
β-strand	199-204	6	12
β-strand	213-214	2	12
β-strand	218	1	8
β-strand	223-233	11	14
β-strand	239-242	4	13
β-strand	243-256	14	12

Chain C: 6 helices, 20 β-strands

Element	Residues	Length	Sheet
β-strand	23	1	4
β-strand	39-40	2	4
β-strand	42	1	3
α-helix	43-45	3
β-strand	51-52	2	16
α-helix	53	1
β-strand	58	1	10
α-helix	65-67	3
β-strand	69-73	5	16
β-strand	81-83	3	17
β-strand	86	1	17
α-helix	94-96	3
α-helix	98-103	6
β-strand	106-110	5	18
β-strand	113-119	7	16
β-strand	126	1	19
β-strand	127-134	8	17
α-helix	144-148	5
β-strand	151-157	7	17
β-strand	162-167	6	16
β-strand	176-177	2	18
β-strand	187-192	6	17
β-strand	197	1	19
β-strand	205-214	10	16
β-strand	219-223	5	18
β-strand	236	1	9

Chain D: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3-4	2	20
β-strand	26-27	2	20
α-helix	35-37	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein VP1	A	protein	289	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP2	B	protein	261	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP3	C	protein	237	Human rhinovirus 2	P04936 (AlphaFold model)
Protein VP4	D	protein	68	Human rhinovirus 2	P04936 (AlphaFold model)
LDL-receptor class A 3	E	protein	39	Homo sapiens	P98155 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>3DPR_1 Protein VP1 (chains A)
NPVENYIDEVLNEVLVVPNINSSNPTTSNSAPALDAAETGHTSSVQPEDVIETRYVQTSQ
TRDEMSLESFLGRSGCIHESKLEVTLANYNKENFTVWAINLQEMAQIRRKFELFTYTRFD
SEITLVPCISALSQDIGHITMQYMYVPPGAPVPNSRDDYAWQSGTNASVFWQHGQAYPRF
SLPFLSVASAYYMFYDGYDEQDQNYGTANTNNMGSLCSRIVTEKHIHKVHIMTRIYHKAK
HVKAWCPRPPRALEYTRAHRTNFKIEDRSIQTAIVTRPIITTAGPSDMY

Sequence of entity 2 (B), FASTA

>3DPR_2 Protein VP2 (chains B)
SPTVEACGYSDRIIQITRGDSTITSQDVANAIVAYGVWPHYLSSKDASAIDKPSQPDTSS
NRFYTLRSVTWSSSSKGWWWKLPDALKDMGIFGENMFYHYLGRSGYTIHVQCNASKFHQG
TLIVALIPEHQIASALHGNVNVGYNYTHPGETGREVKAETRLNPDLQPTEEYWLNFDGTL
LGNITIFPHQFINLRSNNSATIIAPYVNAVPMDSMRSHNNWSLVIIPICPLETSSAINTI
PITISISPMCAEFSGARAKRQ

Sequence of entity 3 (C), FASTA

>3DPR_3 Protein VP3 (chains C)
GLPVFITPGSGQFLTTDDFQSPCALPWYHPTKEISIPGEVKNLVEICQVDSLVPINNTDT
YINSENMYSVVLQSSINAPDKIFSIRTDVASQPLATTLIGEISSYFTHWTGSLRFSFMFC
GTANTTVKLLLAYTPPGIAEPTTRKDAMLGTHVIWDVGLQSTISMVVPWISASHYRNTSP
GRSTSGYITCWYQTRLVIPPQTPPTARLLCFVSGCKDFCLRMARDTNLHLQSGAIAQ

Sequence of entity 4 (D), FASTA

>3DPR_4 Protein VP4 (chains D)
GAQVSRQNVGTHSTQNSVSNGSSLNYFNINYFKDAASNGASKLEFTQDPSKFTDPVKDVL
EKGIPTLQ

Sequence of entity 5 (E), FASTA

>3DPR_5 LDL-receptor class A 3 (chains E)
CRIHEISCGAHSTQCIPVSWRCDGENDCDSGEDEENCGN

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
DAO	Lauric acid	C12 H24 O2	1

Primary citation

Minor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition. Querol-Audi, J., Konecsni, T., Pous, J. et al. FEBS Lett (2009) 583:235-240. DOI 10.1016/j.febslet.2008.12.014 · 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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