4K50: Rhinovirus 16 polymerase elongation complex

Rhinovirus 16 polymerase elongation complex (r1_form). Determined by X-ray diffraction at 2.93 Å resolution. Released 22 May 2013.

Method: X-ray diffraction
Resolution: 2.93 Å
Organism: Human rhinovirus A16
Chains: 12
Atoms: 19,187
Mol. weight: 274.44 kDa
Released: 22 May 2013

Explore 4K50 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4K50 contains 125 α-helices and 92 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: 32 helices, 24 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	1
α-helix	9-12	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	59-61	3
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	4
β-strand	107	1	4
α-helix	108-110	3
α-helix	120-122	3
α-helix	127-130	4
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	165-168	4
α-helix	173-174	2
β-strand	175-178	4	1
α-helix	179-180	2
α-helix	181-200	20
β-strand	203	1	6
β-strand	208	1	6
α-helix	214-217	4
α-helix	221-224	4
β-strand	229-232	4	6
β-strand	233-235	3	7
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-274	6	1
β-strand	277-282	6	1
α-helix	292-311	20
α-helix	317-319	3
β-strand	321-325	5	6
β-strand	328-333	6	6
α-helix	339-344	6
α-helix	347-349	3
β-strand	353-355	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 E: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	10
α-helix	9-12	4
β-strand	26-27	2	11
β-strand	39-40	2	12
α-helix	41-42	2
α-helix	54-58	5
α-helix	59-61	3
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	13
β-strand	107	1	13
α-helix	108-110	3
α-helix	120-122	3
α-helix	127-130	4
β-strand	132	1	14
β-strand	137	1	14
α-helix	139-148	10
α-helix	152-153	2
β-strand	154-158	5	10
β-strand	162-163	2	12
α-helix	165-167	3
α-helix	173-174	2
β-strand	175-178	4	10
α-helix	179-180	2
α-helix	181-199	19
β-strand	203	1	15
β-strand	208	1	15
α-helix	214-224	11
β-strand	229-235	7	15
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-273	5	10
β-strand	277-282	6	10
α-helix	292-311	20
α-helix	317-319	3
β-strand	321-325	5	15
β-strand	328-333	6	15
α-helix	339-344	6
α-helix	347-349	3
β-strand	353-355	3	15
α-helix	356-358	3
β-strand	372	1	16
β-strand	375	1	16
β-strand	376-379	4	17
β-strand	387-390	4	17
α-helix	393-399	7
β-strand	402-403	2	11
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 I: 31 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	18
α-helix	9-12	4
β-strand	26-27	2	19
β-strand	39-40	2	20
α-helix	41-42	2
α-helix	54-58	5
α-helix	59-61	3
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	21
β-strand	107	1	21
α-helix	108-110	3
α-helix	120-122	3
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	154-158	5	18
β-strand	162-163	2	20
α-helix	165-168	4
α-helix	173-174	2
β-strand	175-178	4	18
α-helix	181-199	19
β-strand	203	1	23
β-strand	208	1	23
α-helix	214-217	4
α-helix	221-224	4
β-strand	229-235	7	23
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-273	5	18
β-strand	277-282	6	18
α-helix	292-311	20
α-helix	317-319	3
β-strand	321-325	5	23
β-strand	328-333	6	23
α-helix	339-344	6
α-helix	347-349	3
β-strand	353-355	3	23
α-helix	356-358	3
β-strand	372	1	24
β-strand	375	1	24
β-strand	376-379	4	25
β-strand	387-390	4	25
α-helix	393-399	7
β-strand	402-403	2	19
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 M: 31 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	2-8	7	26
α-helix	9-12	4
β-strand	26-27	2	27
β-strand	39-40	2	28
α-helix	41-42	2
α-helix	54-58	5
α-helix	59-61	3
α-helix	72-86	15
α-helix	97-102	6
β-strand	104	1	29
β-strand	107	1	29
α-helix	108-110	3
α-helix	120-122	3
α-helix	127-130	4
β-strand	132	1	30
β-strand	137	1	30
α-helix	139-148	10
α-helix	152-153	2
β-strand	154-158	5	26
β-strand	162-163	2	28
α-helix	165-167	3
α-helix	173-174	2
β-strand	175-178	4	26
α-helix	179-180	2
α-helix	181-200	20
β-strand	203	1	31
β-strand	208	1	31
α-helix	214-224	11
β-strand	229-235	7	31
α-helix	239-241	3
α-helix	244-256	13
α-helix	265-268	4
β-strand	269-273	5	26
β-strand	277-282	6	26
α-helix	292-311	20
α-helix	317-319	3
β-strand	321-325	5	31
β-strand	328-333	6	31
α-helix	339-344	6
α-helix	347-349	3
β-strand	353-355	3	31
α-helix	356-358	3
β-strand	371-372	2	32
β-strand	375-379	5	32
β-strand	387-390	4	32
α-helix	393-400	8
β-strand	402-403	2	27
α-helix	406-408	3
α-helix	409-420	12
α-helix	421-423	3
α-helix	425-435	11
α-helix	439-443	5
α-helix	449-457	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA polymerase 3D-POL	A, E, I, M	protein	460	Human rhinovirus A16	Q82122 (AlphaFold model)
RNA (33-mer)	B, F, J, N	RNA	35
RNA (5'-r(pgpcpcpcpgpgpapcpgpapgpapgpa)-3')	C, G, K, O	RNA	14

Sequence of entity 1 (A, E, I, M), FASTA

>4K50_1 RNA polymerase 3D-POL (chains A, E, I, M)
GQIQISKHVKDVGLPSIHTPTKTKLQPSVFYDIFPGSKEPAVLTEKDPRLKVDFDSALFS
KYKGNTECSLNEHIQVAVAHYSAQLATLDIDPQPIAMEDSVFGMDGLEALDLNTSAGYPY
VTLGIKKKDLINNKTKDISKLKLALDKYDVDLPMITFLKDELRKKDKIAAGKTRVIEASS
INDTILFRTVYGNLFSKFHLNPGVVTGCAVGCDPETFWSKIPLMLDGDCIMAFDYTNYDG
SIHPIWFKALGMVLDNLSFNPTLINRLCNSKHIFKSTYYEVEGGVPSGCSGTSIFNSMIN
NIIIRTLVLDAYKHIDLDKLKIIAYGDDVIFSYKYKLDMEAIAKEGQKYGLTITPADKSS
EFKELDYGNVTFLKRGFRQDDKYKFLIHPTFPVEEIYESIRWTKKPSQMQEHVLSLCHLM
WHNGPEIYKDFETKIRSVSAGRALYIPPYELLRHEWYEKF

Sequence of entity 2 (B, F, J, N), FASTA

>4K50_2 RNA (33-MER) (chains B, F, J, N)
AGGAGAUGAAAGUCUCCAGGUCUCUCGUCCGGAAA

Sequence of entity 3 (C, G, K, O), FASTA

>4K50_3 RNA (5'-R(P*GP*CP*CP*CP*GP*GP*AP*CP*GP*AP*GP*AP*GP*A)-3') (chains C, G, K, O)
GCCCGGACGAGAGA

Primary citation

Structures of coxsackievirus, rhinovirus, and poliovirus polymerase elongation complexes solved by engineering RNA mediated crystal contacts. Gong, P., Kortus, M.G., Nix, J.C. et al. PLoS One (2013) 8:e60272-e60272. DOI 10.1371/journal.pone.0060272 · 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
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
1D3E 28.0 Å, cryo-EM structure of human rhinovirus 16 (HRV16) complexed with a two-domain fragment of…

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