6SZV: Polymerase acidic protein

Bat Influenza A polymerase elongation complex with incoming UTP analogue (core + endonuclease only). Determined by electron microscopy at 2.5 Å resolution. Released 15 Apr 2020.

Method: Electron microscopy
Resolution: 2.5 Å
Organisms: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)), Influenza B virus
Chains: 6
Atoms: 14,847
Mol. weight: 285.41 kDa
Ligands: 2KH, MG, M4H
Released: 15 Apr 2020

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

Secondary structure: helices and β-sheets

6SZV contains 92 α-helices and 77 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, 32 β-strands

Element	Residues	Length	Sheet
α-helix	3-8	6
α-helix	11-24	14
α-helix	33-49	17
β-strand	52-54	3	1
β-strand	60-62	3	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	116-123	8	2
α-helix	127-137	11
β-strand	144-149	6	2
β-strand	154-155	2	2
β-strand	157	1	3
β-strand	160	1	3
α-helix	165-185	21
α-helix	189-193	5
α-helix	209-215	7
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	4
α-helix	260	1
β-strand	275	1	5
α-helix	276	1
β-strand	290-293	4	6
β-strand	300	1	7
β-strand	302	1	7
α-helix	303-311	9
β-strand	317-324	8	6
α-helix	331-346	16
β-strand	354-355	2	8
α-helix	359-364	6
α-helix	371	1
β-strand	372-373	2	9
α-helix	376-378	3
β-strand	386-387	2	9
α-helix	388-389	2
α-helix	391-395	5
β-strand	397	1	5
α-helix	401-409	9
β-strand	412	1	10
β-strand	416	1	6
α-helix	424-426	3
α-helix	429-445	17
β-strand	448	1	10
α-helix	449-470	22
β-strand	475-476	2	8
β-strand	477-485	9	6
β-strand	491-501	11	6
α-helix	511-512	2
β-strand	513-521	9	6
α-helix	525-532	8
β-strand	536-546	11	6
β-strand	551-565	15	6
α-helix	567-574	8
α-helix	578-598	21
α-helix	603-607	5
β-strand	614-619	6	11
β-strand	622-626	5	11
α-helix	628-644	17
α-helix	648-668	21
β-strand	674-675	2	4
α-helix	678-686	9
α-helix	693-712	20

Chain B: 45 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	11
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	12
β-strand	64-67	4	12
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-114	13
β-strand	118	1	13
α-helix	119-124	6
β-strand	127-130	4	14
β-strand	135-138	4	14
α-helix	139-153	15
α-helix	157-160	4
β-strand	162	1	13
α-helix	163-172	10
α-helix	173-175	3
β-strand	179-193	15	15
β-strand	198-212	15	15
α-helix	214-221	8
β-strand	223-228	6	16
β-strand	240-243	4	16
α-helix	246-263	18
β-strand	269	1	4
α-helix	276-291	16
β-strand	298-304	7	4
β-strand	306	1	17
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	16
β-strand	355-359	5	9
β-strand	364-368	5	9
α-helix	370-375	6
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	16
β-strand	400-402	3	16
α-helix	413-426	14
α-helix	429-432	4
β-strand	436-443	8	4
β-strand	446-453	8	4
α-helix	456-472	17
β-strand	477	1	17
β-strand	483-486	4	4
β-strand	491	1	18
β-strand	496	1	18
β-strand	497	1	19
β-strand	501	1	19
α-helix	502-503	2
α-helix	506-511	6
α-helix	519-536	18
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	613-615	3
α-helix	618-624	7
α-helix	635	1
β-strand	636	1	20
α-helix	637	1
β-strand	656	1	20
α-helix	657	1
β-strand	658	1	21
α-helix	659	1
β-strand	668	1	22
α-helix	669-670	2
α-helix	673-674	2
β-strand	677-678	2	15
α-helix	684-697	14
β-strand	713	1	23
α-helix	714-730	17
α-helix	737-753	17

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	1-11	11
α-helix	14-22	9
β-strand	24	1	23
α-helix	28-32	5
α-helix	43-50	8
β-strand	57-60	4	22
α-helix	63-66	4
β-strand	70	1	24
β-strand	76	1	24
β-strand	78-80	3	22
β-strand	88-91	4	22
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	25
β-strand	141-148	8	26
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-192	13
β-strand	198	1	21
α-helix	200-211	12
β-strand	214-220	7	26
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	25
β-strand	240-245	6	25

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
5' vRNA	V	RNA	14	Influenza B virus
3' vRNA	R	RNA	21	Influenza B virus
Capped mRNA	M	RNA	26	Influenza B virus

Sequence of entity 1 (A), FASTA

>6SZV_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

>6SZV_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

>6SZV_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

>6SZV_4 5' vRNA (chains V)
AGUAGUAACAAGAG

Sequence of entity 5 (R), FASTA

>6SZV_5 3' vRNA (chains R)
UAUACCUCUGCUUCUGCUAUU

Sequence of entity 6 (M), FASTA

>6SZV_6 Capped mRNA (chains M)
XAAUGCUAUAAUAGCAGAAGCAGAGG

Ligands and cofactors

ID	Name	Formula	Copies
2KH	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]uridine	C9 H16 N3 O14 P3	1
MG	Magnesium ion	Mg	5
M4H	5-oxidanyl-4-oxidanylidene-1-[(1-pyrrolo[2,3-b]pyridin-1-ylcyclopentyl)methyl]p…	C19 H19 N3 O4	1

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…
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…
6T0R 2.82 Å, Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with…
6EVK 2.9 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap…

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