1ND2: Rhinovirus 16

Name: PDB 1ND2: The structure of Rhinovirus 16
Published: 2003-12-16
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: virus

The structure of Rhinovirus 16. Determined by X-ray diffraction at 2.5 Å resolution. Released 16 Dec 2003.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Human rhinovirus 16
Chains: 4
Atoms: 6,858
Mol. weight: 95.7 kDa
Ligands: ZN, MYR
Released: 16 Dec 2003

Explore 1ND2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1ND2 contains 38 α-helices and 62 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: 15 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	4-11	8
β-strand	16	1	1
α-helix	17-19	3
β-strand	20	1	2
β-strand	34-35	2	3
α-helix	37-39	3
α-helix	47-49	3
β-strand	56	1	2
β-strand	61	1	1
α-helix	63-65	3
β-strand	66	1	4
α-helix	67-71	5
β-strand	75-83	9	5
α-helix	88-91	4
β-strand	93-97	5	6
α-helix	104-110	7
β-strand	113-130	18	5
β-strand	139-145	7	6
α-helix	150-152	3
α-helix	158-161	4
β-strand	166-171	6	6
α-helix	175-177	3
β-strand	178-181	4	5
β-strand	190-191	2	5
β-strand	196	1	7
β-strand	197	1	8
β-strand	206	1	8
β-strand	216-221	6	6
α-helix	224-225	2
β-strand	230-248	19	5
α-helix	250-251	2
β-strand	252	1	9
β-strand	258	1	10
β-strand	264	1	11
α-helix	270-272	3
α-helix	276-278	3
β-strand	279	1	12

Chain B: 13 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	14-18	5	13
β-strand	21-25	5	13
β-strand	32-33	2	14
α-helix	34-36	3
α-helix	41-43	3
α-helix	52-53	2
β-strand	54	1	14
α-helix	57-59	3
β-strand	64-65	2	14
β-strand	69-71	3	15
β-strand	78-82	5	16
α-helix	84-86	3
α-helix	90-98	9
β-strand	99-111	13	14
β-strand	119-128	10	16
β-strand	135	1	11
α-helix	140-143	4
α-helix	144-147	4
α-helix	150-152	3
β-strand	154-155	2	16
α-helix	165-167	3
α-helix	170-172	3
β-strand	177	1	9
α-helix	179-184	6
β-strand	187-191	5	16
β-strand	197-202	6	14
β-strand	211	1	14
β-strand	216	1	7
β-strand	219-230	12	16
β-strand	238-240	3	15
β-strand	241-254	14	14
α-helix	257-258	2

Chain C: 8 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	6-7	2
β-strand	23	1	5
α-helix	30-33	4
β-strand	39-40	2	5
β-strand	42	1	4
α-helix	44-47	4
β-strand	51-52	2	3
β-strand	58	1	12
α-helix	65-68	4
β-strand	69-72	4	3
β-strand	81-86	6	17
α-helix	98-103	6
β-strand	106-110	5	18
β-strand	113-119	7	3
β-strand	126	1	19
β-strand	128-134	7	17
α-helix	139-141	3
α-helix	144-148	5
β-strand	151-156	6	17
β-strand	162-167	6	3
β-strand	176-177	2	18
α-helix	182-184	3
β-strand	188-193	6	17
β-strand	198	1	19
β-strand	207-215	9	3
β-strand	220-224	5	18
β-strand	237	1	10

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	20
β-strand	27-29	3	20
α-helix	35-37	3
α-helix	40-43	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
coat protein VP1	A	protein	285	Human rhinovirus 16	Q82122 (AlphaFold model)
coat protein VP2	B	protein	261	Human rhinovirus 16	Q82122 (AlphaFold model)
coat protein VP3	C	protein	238	Human rhinovirus 16	Q82122 (AlphaFold model)
coat protein VP4	D	protein	68	Human rhinovirus 16	Q82122 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>1ND2_1 coat protein VP1 (chains A)
NPVERYVDEVLNEVLVVPNINQSHPTTSNAAPVLDAAETGHTNKIQPEDTIETRYVQSSQ
TLDEMSVESFLGRSGCIHESVLDIVDNYNDQSFTKWNINLQEMAQIRRKFEMFTYARFDS
EITMVPSVAAKDGHIGHIVMQYMYVPPGAPIPTTRDDYAWQSGTNASVFWQHGQPFPRFS
LPFLSIASAYYMFYDGYDGDTYKSRYGTVVTNDMGTLCSRIVTSEQLHKVKVVTRIYHKA
KHTKAWCPRPPRAVQYSHTHTTNYKLSSEVHNDVAIRPRTNLTTV

Sequence of entity 2 (B), FASTA

>1ND2_2 coat protein VP2 (chains B)
SPSVEACGYSDRIIQITRGDSTITSQDVANAVVGYGVWPHYLTPQDATAIDKPTQPDTSS
NRFYTLDSKMWNSTSKGWWWKLPDALKDMGIFGENMFYHFLGRSGYTVHVQCNASKFHQG
TLLVVMIPEHQLATVNKGNVNAGYKYTHPGEAGREVGTQVENEKQPSDDNWLNFDGTLLG
NLLIFPHQFINLRSNNSATLIVPYVNAVPMDSMVRHNNWSLVIIPVCQLQSNNISNIVPI
TVSISPMCAEFSGARAKTVVQ

Sequence of entity 3 (C), FASTA

>1ND2_3 coat protein VP3 (chains C)
GLPVYVTPGSGQFMTTDDMQSPCALPWYHPTKEIFIPGEVKNLIEMCQVDTLIPINSTQS
NIGNVSMYTVTLSPQTKLAEEIFAIKVDIASHPLATTLIGEIASYFTHWTGSLRFSFMFC
GTANTTLKVLLAYTPPGIGKPRSRKEAMLGTHVVWDVGLQSTVSLVVPWISASQYRFTTP
DTYSSAGYITCWYQTNFVVPPNTPNTAEMLCFVSGCKDFCLRMARDTDLHKQTGPITQ

Sequence of entity 4 (D), FASTA

>1ND2_4 coat protein VP4 (chains D)
GAQVSRQNVGTHSTQNMVSNGSSLNYFNINYFKDAASSGASRLDFSQDPSKFTDPVKDVL
EKGIPTLQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
MYR	Myristic acid	C14 H28 O2	2

Primary citation

Structural and virological studies of the stages of virus replication that are affected by antirhinovirus compounds. Zhang, Y., Simpson, A.A., Ledford, R.M. et al. J Virol (2004) 78:11061-11069. DOI 10.1128/JVI.78.20.11061-11069.2004 · PubMed

Other PDB entries of the same protein (UniProt Q82122 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1AYM 2.15 Å, Human rhinovirus 16 coat protein at high resolution
1XR7 2.3 Å, Crystal structure of RNA-dependent RNA Polymerase 3D from human rhinovirus serotype 16
1TP7 2.4 Å, Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16
1NCR 2.7 Å, The structure of Rhinovirus 16 when complexed with pleconaril, an antiviral compound
1C8M 2.8 Å, Refined crystal structure of human rhinovirus 16 complexed with VP63843 (pleconaril), an…
1ND3 2.8 Å, The structure of HRV16, when complexed with pleconaril, an antiviral compound
1QJU 2.8 Å, Human rhinovirus 16 coat protein in complex with antiviral compound VP61209
1QJX 2.8 Å, Human rhinovirus 16 coat protein in complex with antiviral compound WIN68934
1QJY 2.8 Å, Human rhinovirus 16 coat protein in complex with antiviral compound VP65099
1AYN 2.9 Å, Human rhinovirus 16 coat protein
4K50 2.93 Å, Rhinovirus 16 polymerase elongation complex (r1_form)
1D3E 28.0 Å, cryo-EM structure of human rhinovirus 16 (HRV16) complexed with a two-domain fragment of…

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