8PNQ: Polymerase acidic protein

Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide mimic bound in site 1A/2A. Determined by electron microscopy at 2.88 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 2.88 Å
Organisms: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)), Homo sapiens
Chains: 6
Atoms: 14,913
Mol. weight: 292.1 kDa
Ligands: 2KH, MG
Released: 21 Feb 2024

Explore 8PNQ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PNQ contains 86 α-helices and 73 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, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-22	12
α-helix	32-49	18
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	84-98	15
α-helix	100-103	4
β-strand	109-111	3	2
β-strand	116-123	8	2
α-helix	127-138	12
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	165-184	20
α-helix	188-193	6
α-helix	194-197	4
α-helix	210-216	7
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	3
β-strand	275	1	4
α-helix	276	1
β-strand	290-293	4	5
α-helix	303-312	10
β-strand	317-324	8	5
α-helix	331-350	20
β-strand	358-360	3	5
α-helix	364-369	6
α-helix	376	1
β-strand	377-380	4	6
α-helix	381-383	3
β-strand	391-392	2	6
α-helix	393-394	2
α-helix	396-400	5
β-strand	402	1	4
α-helix	403-404	2
α-helix	406-414	9
β-strand	417	1	7
α-helix	418	1
β-strand	421	1	5
α-helix	425-427	3
α-helix	429-431	3
α-helix	434-451	18
β-strand	453	1	7
α-helix	454-475	22
β-strand	480-490	11	5
β-strand	496-506	11	5
β-strand	517-526	10	5
α-helix	534-537	4
β-strand	541-551	11	5
β-strand	556-571	16	5
α-helix	572-579	8
α-helix	583-603	21
α-helix	608-609	2
α-helix	610-614	5
β-strand	619-624	6	8
β-strand	627-631	5	8
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	3
α-helix	683-691	9
α-helix	698-715	18

Chain B: 36 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
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	9
β-strand	64-67	4	9
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	10
α-helix	119-124	6
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-152	14
α-helix	157-159	3
β-strand	162	1	10
α-helix	163-173	11
β-strand	178-181	4	12
β-strand	184-192	9	13
β-strand	199-207	9	13
β-strand	210-213	4	12
α-helix	214-221	8
β-strand	223-228	6	14
β-strand	240-244	5	14
α-helix	246-264	19
β-strand	269	1	3
α-helix	276-292	17
β-strand	298-304	7	3
β-strand	306	1	15
α-helix	310-312	3
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	14
β-strand	355-359	5	6
β-strand	364-368	5	6
α-helix	370-375	6
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	14
β-strand	400-402	3	14
α-helix	413-425	13
α-helix	429-432	4
β-strand	437-443	7	3
β-strand	446-453	8	3
α-helix	456-473	18
β-strand	477	1	15
β-strand	483-486	4	3
β-strand	489-492	4	16
β-strand	495-498	4	16
β-strand	501	1	16
α-helix	506-511	6
α-helix	519-535	17
α-helix	541-558	18
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	608-611	4
α-helix	618-624	7
β-strand	636	1	17
α-helix	637	1
β-strand	656	1	17
β-strand	658	1	18
β-strand	667-668	2	19
β-strand	677-678	2	13
α-helix	680-699	20
α-helix	701-703	3
β-strand	713	1	20
α-helix	714-732	19
α-helix	737-755	19

Chain C: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	15-21	7
β-strand	24	1	20
α-helix	25-32	8
α-helix	43-50	8
β-strand	57-60	4	19
α-helix	63-66	4
β-strand	70	1	21
β-strand	76	1	21
β-strand	78-79	2	19
β-strand	88-91	4	19
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	22
β-strand	141-148	8	23
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-193	14
β-strand	198	1	18
α-helix	200-211	12
β-strand	214-220	7	23
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	22
β-strand	240-245	6	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	729	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	M9TI86
RNA-directed RNA polymerase catalytic subunit	B	protein	757	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	M9TLW3
Polymerase basic protein 2	C	protein	788	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	X5F427
51-mer vRNA loop (v51_mut_S)	V	RNA	51	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Replication product	M	RNA	33	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
RNA Pol II CTD 6 repeats (site 1A/2A)	G	protein	42	Homo sapiens	P24928 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PNQ_1 Polymerase acidic protein (chains A)
MHHHHHHHHGSGSMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFM
YSDFHFIDERGESTIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLP
DLYDYKENRFIEIGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEES
RARIKTRLFTIRQEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLE
NFRAYVDGFEPNGCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDA
LKLSIEDPSHEGEGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQD
IKNEEKIPRTKNMKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWI
QSEFNKACELTDSSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINT
ALLNASCAAMDDFQLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSL
TDPRLEPHKWEKYCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQ
SLQQIESMIEAESSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFN
SLYASPQLEGFSAESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWF
NSFLTHALR

Sequence of entity 2 (B), FASTA

>8PNQ_2 RNA-directed RNA polymerase catalytic subunit (chains B)
MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Sequence of entity 3 (C), FASTA

>8PNQ_3 Polymerase basic protein 2 (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSA
WSHPQFEK

Sequence of entity 4 (V), FASTA

>8PNQ_4 51-mer vRNA loop (v51_mut_S) (chains V)
AGUAGAAACAAGGGUGUAUUUUCCCCUCUUUUUGUUUCCCCUGCUUUUGCU

Sequence of entity 5 (M), FASTA

>8PNQ_5 Replication product (chains M)
AGCAAAAGCAGGGGAAACAAAAAGAGGGGAAAA

Sequence of entity 6 (G), FASTA

>8PNQ_6 RNA Pol II CTD 6 repeats (site 1A/2A) (chains G)
YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

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	2

Primary citation

The host RNA polymerase II C-terminal domain is the anchor for replication of the influenza virus genome. Krischuns, T., Arragain, B., Isel, C. et al. Nat Commun (2024) 15:1064-1064. DOI 10.1038/s41467-024-45205-2 · PubMed

Other PDB entries of the same protein (UniProt M9TI86), best resolution first:

9RAG 1.99 Å, Influenza A/H7N9 polymerase in complex with a 70-mer RNA template, in stalled elongation.
9RAF 2.15 Å, Influenza A/H7N9 polymerase in complex with a 70-mer template in stalled elongation with…
7QTL 2.48 Å, Influenza A/H7N9 polymerase elongation complex
8PNP 2.49 Å, Influenza A/H7N9 polymerase in pre-initiation state with continuous Pol II pS5 CTD…
7R0E 2.51 Å, Early transcription elongation state of influenza A/H7N9 polymerase backtracked due to…
8RMQ 2.54 Å, Influenza polymerase A/H7N9-4M (ENDO(R) | Core2)
8RMP 2.77 Å, Influenza polymerase A/H7N9-4M (ENDO(R) | Core1)
7ZPM 2.81 Å, Influenza A/H7N9 polymerase apo-protein dimer complex
8BEK 2.86 Å, Early transcription elongation state of influenza A/H7N9 backtracked polymerase with…
8PM0 2.9 Å, Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with…
9G0A 3.1 Å, Influenza A/H7N9 polymerase post-cleavage cap-snatching complex
7ZPL 3.12 Å, Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook

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