9F2R: Polymerase acidic protein

Influenza A/H17N10 polymerase with bound promoter and 3' end of template in active site. Determined by X-ray diffraction at 1.96 Å resolution. Released 18 Sept 2024.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Influenza A virus
Chains: 5
Atoms: 19,393
Mol. weight: 277.07 kDa
Ligands: MGT, MG
Released: 18 Sept 2024

Explore 9F2R in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9F2R contains 118 α-helices and 105 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: 36 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-22	12
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	84-98	15
α-helix	100-103	4
β-strand	109-111	3	2
β-strand	116-123	8	2
α-helix	127-137	11
β-strand	143-149	7	2
β-strand	154-156	3	2
β-strand	157	1	3
β-strand	160	1	3
α-helix	165-183	19
α-helix	188-191	4
α-helix	209-216	8
α-helix	226-235	10
α-helix	241-246	6
α-helix	256-257	2
β-strand	258-259	2	4
α-helix	262-264	3
α-helix	265-271	7
β-strand	274-275	2	5
α-helix	276	1
β-strand	290-293	4	6
α-helix	303-311	9
β-strand	317-324	8	6
α-helix	331-347	17
β-strand	354-355	2	7
α-helix	359-364	6
α-helix	371	1
β-strand	372-373	2	8
α-helix	376-378	3
β-strand	386-387	2	8
α-helix	392-395	4
β-strand	396-397	2	5
α-helix	401-409	9
β-strand	412	1	9
β-strand	415-416	2	6
α-helix	420-426	7
α-helix	429-445	17
β-strand	448	1	9
α-helix	449-470	22
β-strand	475-476	2	7
β-strand	477-486	10	6
β-strand	491-501	11	6
α-helix	511	1
β-strand	512-521	10	6
α-helix	525-527	3
α-helix	529-532	4
α-helix	535	1
β-strand	536-546	11	6
β-strand	551-566	16	6
α-helix	567-574	8
α-helix	578-598	21
α-helix	603-608	6
β-strand	614-618	5	10
β-strand	623-626	4	10
α-helix	628-644	17
α-helix	648-668	21
β-strand	674-675	2	4
α-helix	678-686	9
α-helix	693-711	19

Chain B: 44 helices, 31 β-strands

Element	Residues	Length	Sheet
α-helix	1	1
β-strand	2-3	2	10
α-helix	5-10	6
α-helix	14-21	8
α-helix	27-29	3
α-helix	36-48	13
β-strand	54-57	4	11
β-strand	64-67	4	11
α-helix	73-74	2
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	12
α-helix	119-123	5
β-strand	127-130	4	13
β-strand	135-138	4	13
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	12
α-helix	163-173	11
β-strand	180-183	4	14
β-strand	208-211	4	14
α-helix	214-221	8
β-strand	223-228	6	15
α-helix	229-230	2
β-strand	240-244	5	15
β-strand	245	1	13
α-helix	246-264	19
β-strand	269	1	4
α-helix	275-292	18
β-strand	298-305	8	4
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	8
β-strand	364-368	5	8
α-helix	371-374	4
α-helix	378-380	3
α-helix	383-393	11
β-strand	396-397	2	15
β-strand	400-402	3	15
α-helix	413-425	13
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	16
β-strand	483-486	4	4
β-strand	489-492	4	17
β-strand	495-498	4	17
β-strand	501-502	2	17
α-helix	505-511	7
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-581	9
α-helix	586-588	3
α-helix	591-593	3
α-helix	595-597	3
α-helix	601-603	3
α-helix	608-612	5
α-helix	613-615	3
α-helix	618-624	7
α-helix	637-639	3
β-strand	642-645	4	18
β-strand	653-656	4	18
β-strand	667-668	2	19
α-helix	669-671	3
α-helix	673-676	4
α-helix	678-680	3
α-helix	681-699	19
α-helix	701-704	4
β-strand	713	1	20
α-helix	714-730	17
α-helix	737-753	17

Chain C: 38 helices, 44 β-strands

Element	Residues	Length	Sheet
α-helix	1-12	12
α-helix	14-22	9
β-strand	24	1	20
α-helix	25-31	7
α-helix	43-50	8
β-strand	57-59	3	19
α-helix	63-66	4
β-strand	70	1	21
β-strand	76	1	21
β-strand	78-82	5	19
α-helix	83	1
β-strand	89-91	3	19
α-helix	94-102	9
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	22
β-strand	141-146	6	23
β-strand	154	1	24
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-192	13
α-helix	200-211	12
β-strand	212	1	24
β-strand	215-220	6	23
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	22
β-strand	240-245	6	22
α-helix	249-251	3
α-helix	252-270	19
α-helix	276-286	11
β-strand	288-289	2	25
β-strand	292-293	2	25
α-helix	294-300	7
α-helix	306-314	9
β-strand	319	1	26
β-strand	323-325	3	27
β-strand	328-335	8	27
β-strand	338-341	4	27
β-strand	355-365	11	27
β-strand	370-378	9	27
β-strand	383-388	6	27
α-helix	391-405	15
α-helix	408-411	4
β-strand	421	1	28
β-strand	427	1	28
α-helix	430-440	11
α-helix	443-446	4
β-strand	452	1	29
β-strand	462-463	2	30
β-strand	469-470	2	30
β-strand	474	1	29
β-strand	478-480	3	27
α-helix	492-493	2
β-strand	494	1	26
α-helix	495	1
β-strand	496-498	3	31
β-strand	504-506	3	31
β-strand	511-513	3	31
α-helix	515-517	3
β-strand	529-530	2	25
α-helix	542-555	14
α-helix	557-566	10
α-helix	568-572	5
α-helix	575-577	3
α-helix	578-581	4
α-helix	586-588	3
α-helix	589-605	17
α-helix	612-618	7
α-helix	619-622	4
β-strand	635-640	6	32
β-strand	643-648	6	32
β-strand	656-659	4	33
β-strand	664-667	4	33
β-strand	670-671	2	33
β-strand	687	1	34
β-strand	694-699	6	34
α-helix	702-704	3
β-strand	707-708	2	34
α-helix	713-715	3
β-strand	721-727	7	34
β-strand	730-736	7	34

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	738	Influenza A virus	H6QM92
RNA-directed RNA polymerase catalytic subunit	B	protein	776	Influenza A virus	H6QM91
Polymerase basic protein 2	C	protein	809	Influenza A virus	H6QM90
3' end of the promoter vRNA	R	RNA	21	Influenza A virus
5' end of the promoter vRNA	V	RNA	16	Influenza A virus

Sequence of entity 1 (A), FASTA

>9F2R_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

>9F2R_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

>9F2R_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 (R), FASTA

>9F2R_4 3' end of the promoter vRNA (chains R)
UAUACCUCUGCUUCUGCUAUU

Sequence of entity 5 (V), FASTA

>9F2R_5 5' end of the promoter vRNA (chains V)
AGUAGUAACAAGAGGG

Ligands and cofactors

ID	Name	Formula	Copies
MGT	7N-methyl-8-hydroguanosine-5'-triphosphate	C11 H20 N5 O14 P3	1
MG	Magnesium ion	Mg	1

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

Primary citation

High-resolution structure of a replication-initiation like configuration of influenza polymerase active site visualises the essential role of a conserved dibasic motif in the PA subunit. Drncova, P., Krischuns, T., Naffakh, N. et al. bioRxiv (2024). DOI 10.1101/2023.11.20.567839

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…
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…
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…

Browse structure collections

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