1TP7: Genome polyprotein

Crystal Structure of the RNA-dependent RNA Polymerase from Human Rhinovirus 16. Determined by X-ray diffraction at 2.4 Å resolution. Released 21 Jun 2005.

Method: X-ray diffraction
Resolution: 2.4 Å
Organism: Human rhinovirus 16
Chains: 4
Atoms: 15,051
Mol. weight: 211.89 kDa
Ligands: DMX
Released: 21 Jun 2005

Explore 1TP7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1TP7 contains 116 α-helices and 97 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: 27 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	15-18	4
β-strand	26-27	2	2
β-strand	39-40	2	3
α-helix	41-42	2
α-helix	54-58	5
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	4
β-strand	107	1	4
α-helix	108-111	4
α-helix	120-122	3
α-helix	127-129	3
β-strand	132	1	5
β-strand	137	1	5
α-helix	139-148	10
α-helix	152-153	2
β-strand	154-158	5	1
β-strand	162-163	2	3
α-helix	165-169	5
β-strand	175-178	4	1
α-helix	181-200	20
β-strand	203	1	6
β-strand	208	1	6
α-helix	214-224	11
β-strand	231-232	2	6
β-strand	234-236	3	7
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-273	5	1
β-strand	277-282	6	1
α-helix	293-311	19
α-helix	317-319	3
β-strand	321-325	5	6
β-strand	328-332	5	6
α-helix	339-347	9
β-strand	352-354	3	7
α-helix	356-358	3
β-strand	372	1	8
β-strand	375	1	8
β-strand	376-379	4	9
β-strand	387-390	4	9
α-helix	393-400	8
β-strand	402-403	2	2
α-helix	406-408	3
α-helix	409-420	12
α-helix	421-423	3
α-helix	425-435	11
α-helix	439-442	4
α-helix	449-457	9

Chain B: 27 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	2-5	4	10
β-strand	8	1	11
α-helix	9-12	4
β-strand	26-27	2	12
α-helix	28	1
β-strand	39-40	2	13
α-helix	55-59	5
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	14
β-strand	107	1	14
α-helix	108-111	4
α-helix	120-122	3
α-helix	127-130	4
β-strand	132	1	15
β-strand	137	1	15
α-helix	139-148	10
β-strand	154-158	5	10
β-strand	162-163	2	13
α-helix	165-168	4
β-strand	175-178	4	10
α-helix	181-200	20
β-strand	203	1	16
β-strand	208	1	16
α-helix	214-217	4
α-helix	221-224	4
β-strand	230-233	4	16
β-strand	234-235	2	17
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	271-273	3	10
β-strand	277	1	11
β-strand	278-282	5	10
α-helix	292-311	20
α-helix	317-319	3
β-strand	321-325	5	16
β-strand	328-332	5	16
α-helix	339-347	9
β-strand	353-354	2	17
α-helix	356-358	3
β-strand	371-372	2	18
β-strand	375-379	5	18
β-strand	387-390	4	18
α-helix	393-400	8
β-strand	402-403	2	12
α-helix	406-408	3
α-helix	409-420	12
α-helix	421-423	3
α-helix	425-436	12
α-helix	439-442	4
α-helix	449-457	9

Chain C: 29 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	19
α-helix	9-12	4
β-strand	26-27	2	20
α-helix	28	1
β-strand	39-40	2	21
α-helix	41-42	2
α-helix	54-58	5
α-helix	72-86	15
α-helix	97-102	6
α-helix	108-111	4
α-helix	127-129	3
β-strand	132	1	22
β-strand	137	1	22
α-helix	139-148	10
α-helix	152-153	2
β-strand	154-156	3	19
β-strand	162-163	2	21
α-helix	165-168	4
β-strand	177-178	2	19
α-helix	181-200	20
β-strand	203	1	23
β-strand	208	1	23
α-helix	214-217	4
α-helix	221-224	4
β-strand	231-232	2	23
β-strand	233-235	3	24
α-helix	238-241	4
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-273	5	19
β-strand	277-282	6	19
α-helix	293-311	19
α-helix	317-319	3
β-strand	322-325	4	23
β-strand	328-331	4	23
α-helix	339-345	7
α-helix	347-349	3
β-strand	353-355	3	24
α-helix	356-358	3
α-helix	363-365	3
β-strand	372	1	25
β-strand	375	1	25
β-strand	376-379	4	26
β-strand	387-390	4	26
α-helix	393-400	8
β-strand	402-403	2	20
α-helix	406-408	3
α-helix	410-420	11
α-helix	425-435	11
α-helix	439-442	4
α-helix	449-459	11

Chain D: 33 helices, 26 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	27
α-helix	9-12	4
α-helix	14-17	4
β-strand	26-27	2	28
α-helix	31-33	3
β-strand	39-40	2	29
α-helix	54-58	5
α-helix	72-84	13
α-helix	97-101	5
β-strand	104	1	30
β-strand	107	1	30
α-helix	108-111	4
α-helix	120-122	3
α-helix	127-129	3
β-strand	132	1	31
β-strand	137	1	31
α-helix	139-147	9
α-helix	153	1
β-strand	154-158	5	32
β-strand	162-163	2	29
α-helix	166-170	5
β-strand	175-178	4	32
α-helix	179-180	2
α-helix	181-190	10
α-helix	192-199	8
β-strand	203	1	33
β-strand	208	1	33
α-helix	214-217	4
α-helix	218-220	3
β-strand	229-232	4	33
α-helix	238-241	4
α-helix	244-255	12
α-helix	265-268	4
β-strand	269	1	27
β-strand	272-273	2	32
β-strand	278-279	2	32
β-strand	281-282	2	27
α-helix	293-311	19
α-helix	317-319	3
β-strand	320-324	5	33
β-strand	329-333	5	33
α-helix	339-343	5
α-helix	344-348	5
α-helix	354-355	2
α-helix	356-358	3
β-strand	372	1	34
β-strand	375	1	34
β-strand	376	1	35
β-strand	379	1	36
β-strand	387	1	36
β-strand	390	1	35
α-helix	391-392	2
α-helix	393-399	7
β-strand	402-403	2	28
α-helix	406-408	3
α-helix	409-420	12
α-helix	421-423	3
α-helix	425-435	11
α-helix	449-458	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A, B, C, D	protein	460	Human rhinovirus 16	Q82122 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>1TP7_1 Genome polyprotein (chains A, B, C, D)
GQIQISKHVKDVGLPSIHTPTKTKLQPSVFYDIFPGSKEPAVLTEKDPRLKVDFDSALFS
KYKGNTECSLNEHIQVAVAHYSAQLATLDIDPQPIAMEDSVFGMDGLEALDLNTSAGYPY
VTLGIKKKDLINNKTKDISKLKLALDKYDVDLPMITFLKDELRKKDKIAAGKTRVIEASS
INDTILFRTVYGNLFSKFHLNPGVVTGCAVGCDPETFWSKIPLMLDGDCIMAFDYTNYDG
SIHPIWFKALGMVLDNLSFNPTLINRLCNSKHIFKSTYYEVEGGVPSGCSGTSIFNSMIN
NIIIRTLVLDAYKHIDLDKLKIIAYGDDVIFSYKYKLDMEAIAKEGQKYGLTITPADKSS
EFKELDYGNVTFLKRGFRQDDKYKFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLM
WHNGPEIYKDFETKIRSVSAGRALYIPPYELLRHEWYEKF

Ligands and cofactors

ID	Name	Formula	Copies
DMX	3-[benzyl(dimethyl)ammonio]propane-1-sulfonate	C12 H19 N O3 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Crystal structure of complete rhinovirus RNA polymerase suggests front loading of protein primer. Appleby, T.C., Luecke, H., Shim, J.H. et al. J Virol (2005) 79:277-288. DOI 10.1128/JVI.79.1.277-288.2005 · 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
1ND2 2.5 Å, The structure of 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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