8PM0: Polymerase acidic protein

Influenza A/H7N9 polymerase in replicase-like conformation in pre-initiation state with Pol II pS5 CTD peptide mimic bound in site 1A/2A. Determined by electron microscopy at 2.9 Å resolution. Released 21 Feb 2024.

Method: Electron microscopy
Resolution: 2.9 Å
Organisms: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)), Homo sapiens
Chains: 6
Atoms: 16,669
Mol. weight: 285.64 kDa
Ligands: MG
Released: 21 Feb 2024

Explore 8PM0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PM0 contains 103 α-helices and 91 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, 25 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
α-helix	11-23	13
α-helix	33-49	17
β-strand	76-78	3	1
α-helix	84-98	15
α-helix	100-103	4
β-strand	109-111	3	1
β-strand	116-123	8	1
α-helix	127-138	12
β-strand	143-149	7	1
β-strand	154-156	3	1
α-helix	157-159	3
α-helix	165-185	21
α-helix	209-216	8
α-helix	226-234	9
α-helix	241-248	8
α-helix	256-257	2
β-strand	258-259	2	2
β-strand	275	1	3
α-helix	276	1
β-strand	287	1	4
β-strand	290-293	4	4
α-helix	303-312	10
β-strand	317-324	8	4
α-helix	331-349	19
β-strand	358-360	3	4
α-helix	361	1
α-helix	364-369	6
α-helix	376	1
β-strand	377-378	2	5
α-helix	381-383	3
β-strand	391-392	2	5
α-helix	393-394	2
α-helix	396-400	5
β-strand	402	1	3
α-helix	406-414	9
β-strand	417	1	6
β-strand	421	1	4
α-helix	425-427	3
α-helix	429-431	3
α-helix	434-451	18
β-strand	453	1	6
α-helix	454-475	22
β-strand	480-490	11	4
β-strand	496-506	11	4
β-strand	517-526	10	4
α-helix	530-532	3
α-helix	534-537	4
β-strand	540-551	12	4
β-strand	556-571	16	4
α-helix	572-579	8
α-helix	581-583	3
α-helix	584-600	17
α-helix	608-614	7
β-strand	619-624	6	7
β-strand	627-631	5	7
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	2
α-helix	683-691	9
α-helix	698-714	17

Chain B: 40 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	7
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	8
β-strand	64-67	4	8
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	9
α-helix	119-123	5
β-strand	128-130	3	10
β-strand	135-137	3	10
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	9
α-helix	163-174	12
β-strand	178-183	6	11
β-strand	208-213	6	11
α-helix	214-221	8
β-strand	223-228	6	12
β-strand	240-244	5	12
β-strand	245	1	10
α-helix	249-264	16
β-strand	269	1	2
α-helix	275-290	16
β-strand	298-302	5	2
β-strand	305	1	2
β-strand	306	1	13
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	12
β-strand	354-359	6	5
β-strand	364-369	6	5
α-helix	370-372	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	12
β-strand	400-402	3	12
α-helix	415-425	11
α-helix	429-432	4
β-strand	437-443	7	2
β-strand	446-453	8	2
α-helix	456-472	17
β-strand	477	1	13
α-helix	479-481	3
β-strand	483-486	4	2
β-strand	489-492	4	14
β-strand	495-498	4	14
β-strand	501	1	14
α-helix	502-503	2
α-helix	506-511	6
α-helix	519-535	17
α-helix	541-559	19
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	608-611	4
α-helix	613-615	3
α-helix	618-624	7
α-helix	637-639	3
β-strand	642-645	4	15
β-strand	653-656	4	15
β-strand	667-668	2	16
α-helix	673-676	4
α-helix	680-699	20
α-helix	701-704	4
β-strand	713	1	17
α-helix	714-731	18
α-helix	737-755	19

Chain C: 27 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	17
α-helix	25-31	7
α-helix	38-40	3
α-helix	43-50	8
β-strand	57-59	3	16
α-helix	63-66	4
β-strand	70	1	18
β-strand	76	1	18
β-strand	78-82	5	16
α-helix	83	1
β-strand	89-91	3	16
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-127	12
β-strand	129-135	7	19
β-strand	141-145	5	20
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-192	13
α-helix	200-211	12
β-strand	216-220	5	20
α-helix	229-231	3
α-helix	232-235	4
β-strand	236	1	19
β-strand	240-245	6	19
α-helix	251-272	22
α-helix	276-285	10
β-strand	287-289	3	21
β-strand	292-293	2	21
α-helix	294-298	5
α-helix	306-315	10
β-strand	319-320	2	22
α-helix	322	1
β-strand	323-325	3	23
β-strand	328-335	8	23
β-strand	338-345	8	24
β-strand	351-358	8	24
β-strand	361-366	6	23
β-strand	370-377	8	23
β-strand	380-388	9	23
α-helix	391-405	15
α-helix	408-411	4
β-strand	421	1	25
β-strand	427	1	25
α-helix	428-429	2
α-helix	430-440	11
α-helix	443-447	5
β-strand	452-453	2	26
β-strand	460-461	2	23
β-strand	462-463	2	27
β-strand	469-470	2	27
β-strand	473-474	2	26
β-strand	478-481	4	23
β-strand	493-494	2	22
β-strand	496-498	3	28
β-strand	504-506	3	28
β-strand	511-513	3	28
α-helix	515-517	3
β-strand	529-531	3	21

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))
RNA Pol II CTD 6 repeats (site 1A/2A)	G, P	protein	42	Homo sapiens	P24928 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PM0_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

>8PM0_2 RNA-directed RNA polymerase catalytic subunit (chains B)
MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELKKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Sequence of entity 3 (C), FASTA

>8PM0_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

>8PM0_4 51-mer vRNA loop (v51_mut_S) (chains V)
AGUAGAAACAAGGGUGUAUUUUCCCCUCUUUUUGUUUCCCCUGCUUUUGCU

Sequence of entity 5 (G, P), FASTA

>8PM0_5 RNA Pol II CTD 6 repeats (site 1A/2A) (chains G, P)
YSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPS

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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…
8PNQ 2.88 Å, Influenza A/H7N9 polymerase in elongation state with continuous Pol II pS5 CTD peptide…
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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