6T0R: Polymerase acidic protein

Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with mutated oligo(U) sequence. Determined by electron microscopy at 2.82 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 2.82 Å
Organisms: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)), synthetic construct
Chains: 4
Atoms: 14,120
Mol. weight: 278.47 kDa
Released: 15 Apr 2020

Explore 6T0R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6T0R contains 88 α-helices and 78 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 A: 33 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	11-24	14
α-helix	33-49	17
β-strand	53-54	2	1
β-strand	60-61	2	1
β-strand	73-74	2	1
β-strand	76-78	3	2
α-helix	84-97	14
α-helix	100-103	4
β-strand	109-111	3	2
β-strand	116-122	7	2
α-helix	127-137	11
β-strand	143-148	6	2
β-strand	155-156	2	2
α-helix	157-159	3
α-helix	165-185	21
α-helix	189-192	4
α-helix	209-215	7
α-helix	226-234	9
α-helix	241-247	7
β-strand	258-259	2	3
α-helix	260	1
β-strand	274-275	2	4
α-helix	276-278	3
β-strand	290-293	4	5
α-helix	303-311	9
β-strand	317	1	5
β-strand	322-324	3	5
α-helix	331-346	16
β-strand	354-355	2	6
α-helix	359-364	6
α-helix	371	1
β-strand	372-374	3	7
β-strand	385-387	3	7
α-helix	388-389	2
α-helix	391-395	5
β-strand	396-397	2	4
α-helix	400-409	10
β-strand	412	1	8
β-strand	416	1	5
α-helix	420-422	3
α-helix	424-426	3
α-helix	429-445	17
β-strand	448	1	8
α-helix	449-470	22
β-strand	475-476	2	6
β-strand	477-485	9	5
β-strand	491-501	11	5
α-helix	511-512	2
β-strand	513-521	9	5
β-strand	536-546	11	5
β-strand	551-565	15	5
α-helix	567-574	8
α-helix	578-598	21
α-helix	604-607	4
β-strand	614-619	6	9
β-strand	622-626	5	9
α-helix	628-644	17
α-helix	648-668	21
β-strand	674-675	2	3
α-helix	678-687	10
α-helix	693-711	19

Chain B: 41 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-10	6
α-helix	15-21	7
α-helix	27-29	3
α-helix	36-48	13
β-strand	54-57	4	10
β-strand	64-67	4	10
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-114	13
β-strand	118	1	11
α-helix	119-123	5
β-strand	128-130	3	12
β-strand	135-137	3	12
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-172	10
α-helix	173-175	3
β-strand	180-183	4	13
β-strand	186-192	7	14
β-strand	199-205	7	14
β-strand	208-211	4	13
α-helix	214-221	8
β-strand	223-228	6	15
α-helix	229-230	2
β-strand	240-243	4	15
α-helix	249-263	15
β-strand	269	1	3
α-helix	276-288	13
β-strand	298-304	7	3
β-strand	306	1	16
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	15
β-strand	355-359	5	7
β-strand	364-368	5	7
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	15
β-strand	400-401	2	15
α-helix	413-426	14
α-helix	429-432	4
β-strand	436-442	7	3
β-strand	447-453	7	3
α-helix	456-472	17
β-strand	477	1	16
β-strand	483-486	4	3
β-strand	489-491	3	17
β-strand	495-498	4	17
β-strand	501-504	4	17
α-helix	508-510	3
α-helix	519-535	17
α-helix	541-558	18
α-helix	573-581	9
α-helix	586-588	3
α-helix	591-593	3
α-helix	595-597	3
α-helix	608-611	4
α-helix	618-624	7
α-helix	633-635	3
β-strand	636	1	18
β-strand	656	1	18
α-helix	657	1
β-strand	658	1	19
α-helix	659	1
β-strand	668	1	20
α-helix	669-670	2
β-strand	677-678	2	14
α-helix	684-699	16
β-strand	713	1	21
α-helix	714-731	18
α-helix	737-755	19

Chain C: 14 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	2-11	10
α-helix	14-22	9
β-strand	24	1	21
α-helix	31-33	3
α-helix	43-51	9
β-strand	57-59	3	20
α-helix	63-66	4
β-strand	70	1	22
β-strand	76	1	22
β-strand	78-79	2	20
β-strand	81	1	23
β-strand	84	1	23
β-strand	89-91	3	20
α-helix	93-102	10
α-helix	110-114	5
α-helix	116-126	11
β-strand	129-133	5	24
β-strand	141-148	8	25
α-helix	156-166	11
α-helix	169-171	3
α-helix	180-192	13
β-strand	198	1	19
α-helix	200-211	12
β-strand	214-220	7	25
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	26
β-strand	241	1	26
β-strand	242-245	4	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	738	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM92
RNA-directed RNA polymerase catalytic subunit	B	protein	776	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM91
Polymerase basic protein 2	C	protein	809	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM90
vRNA	V	RNA	44	synthetic construct

Sequence of entity 1 (A), FASTA

>6T0R_1 Polymerase acidic protein (chains A)
GSHHHHHHHHGSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCF
MYSDFHFIDLEGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFL
PDLYDYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEE
SRARIKTRLFVLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDY
HQFKAYVSSFKANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMD
AMKLSVLNPAHEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIK
EMEGKFLNLKKTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEF
NKASELTNSNWIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLN
SSCTAMEEYQVIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPR
NEIHKWEKYCVLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQ
VESMIEAESAVKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYA
SAQLEGFSAESRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFL
KAVQLSMGSGSGENLYFQ

Sequence of entity 2 (B), FASTA

>6T0R_2 RNA-directed RNA polymerase catalytic subunit (chains B)
GSGSGSGSGMDVNPMLIFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVIRTHDYSS
RGIWKTNSETGAQQLNPIDGPLPEDNEPSGYAQTDCVLELIEGLDRSHPGLFETACQETI
DAIQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRKNGYKLNESGRLIDFLKDVL
LSFENDSMEVTTHFQKKKRIRDNHSKKMITQRTIGKKRVKLTKKNYLIRALTLNTMTKDA
ERGKLKRRAIATPGMQIRGFVYFVELLARNICERLEQSGLPVGGNEKKAKLANVIKKMMA
KSTDEELSYTITGDNTKWNENQNPRIFLAMVLRITAGQPEWFRDLLAVAPIMFSNKVARL
GRGYMFESKSMHLRTQISAENLSDINLRYFNEDTKKKIEKIRHLMVEGTASLSPGMMMGM
FNMLSTVLGVSVLNLGQREILKRTYWWDGLQSSDDFALIINGHFKEDIQQGVNHFYRTCK
LVGINMSQKKSYINKTGTFEFTSFFYRYGFVANFSMELPSFGVAGNNESADMSIGTTVIK
TNMINNDLGPATAQMAIQLFIKDYRYTYRCHRGDTNLETRRTKSIKRLWTETISKAGLLV
ADGGPNPYNLRNLHIPEVCLKWSLMDPDYRGRLCNPNNPFVHHMEVESTNLAVVMPAHGP
AKSLEYDAVATTHSWTPKRNRSILNTNQRGILEDERIYQKCCQVFEKFFPSSTYRRPIGM
ASMLDAMLSRARIDARIDLESGRISSQDFSEITNTCKAIEALKRQGSGSGENLYFQ

Sequence of entity 3 (C), FASTA

>6T0R_3 Polymerase basic protein 2 (chains C)
GSGSGSGSGMERIKELMEMVKNSRMREILTTTSVDHMAVIKKYTSGRQEKNPALRMKWMM
AMKYPISASSRIREMIPEKDEDGNTLWTNTKDAGSNRVLVSPNAVTWWNRAGPVSDVVHY
PRVYKMYFDRLERLTHGTFGPVKFYNQVKVRKRVDINPGHKDLTSREAQEVIMEVVFPNE
VGARTLSSDAQLTITKEKKEELKNCKISPIMVAYMLERELVRRTRFLPIAGATSSTYVEV
LHLTQGTCWEQQYTPGGEAENDDLDQTLIIASRNIVRRSIVAIDPLASLLSMCHTTSISS
EPLVEILRSNPTDEQAVNICKAALGIRINNSFSFGGYNFKRVKGSSQRTEKAVLTGNLQT
LTMTIFEGYEEFNVSGKRASAVLKKGAQRLIQAIIGGRTLEDILNLMITLMVFSQEEKML
KAVRGDLNFVNRANQRLNPMYQLLRHFQKDSSTLLKNWGTEEIDPIMGIAGIMPDGTINK
TQTLMGVRLSQGGVDEYSFNERIRVNIDKYLRVRNEKGELLISPEEVSEAQGQEKLPINY
NSSLMWEVNGPESILTNTYHWIIKNWELLKTQWMTDPTVLYNRIEFEPFQTLIPKGNRAI
YSGFTRTLFQQMRDVEGTFDSIQIIKLLPFSAHPPSLGRTQFSSFTLNIRGAPLRLLIRG
NSQVFNYNQMENVIIVLGKSVGSPERSILTESSSIESAVLRGFLILGKANSKYGPVLTIG
ELDKLGRGEKANVLIGQGDTVLVMKRKRDSSILTDSQTALKRIRLEESKGWSHPQFEKGG
GSGGGSGGSAWSHPQFEKGRSGGENLYFQ

Sequence of entity 4 (V), FASTA

>6T0R_4 vRNA (chains V)
AGUAGUAACAAGAGCAAUGUGUCCGUCUCGCCUCUGCUUCUGCU

Primary citation

A Structure-Based Model for the Complete Transcription Cycle of Influenza Polymerase. Wandzik, J.M., Kouba, T., Karuppasamy, M. et al. Cell (2020) 181:877. DOI 10.1016/j.cell.2020.03.061 · PubMed

Other PDB entries of the same protein (UniProt H6QM92), best resolution first:

9F37 1.91 Å, Replication-like initiation state of influenza polymerase with GTP and CTP at…
9F2R 1.96 Å, Influenza A/H17N10 polymerase with bound promoter and 3' end of template in active site
6SZU 2.41 Å, Bat Influenza A polymerase pre-termination complex with pyrophosphate using 44-mer vRNA…
5M3H 2.5 Å, Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5…
6SZV 2.5 Å, Bat Influenza A polymerase elongation complex with incoming UTP analogue (core +…
6T0N 2.54 Å, Bat Influenza A polymerase pre-initiation complex
4WSB 2.65 Å, Bat Influenza A polymerase with bound vRNA promoter
4NFZ 2.7 Å, Crystal structure of polymerase subunit PA N-terminal endonuclease domain from…
6FHH 2.7 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to…
6TW1 2.7 Å, Bat Influenza A polymerase termination complex with pyrophosphate using 44-mer vRNA…
6FHI 2.8 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to…
6EVK 2.9 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap…

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