7ZPM: Polymerase acidic protein

Influenza A/H7N9 polymerase apo-protein dimer complex. Determined by electron microscopy at 2.81 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 2.81 Å
Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Chains: 6
Atoms: 19,330
Mol. weight: 510.87 kDa
Released: 28 Dec 2022

Explore 7ZPM in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7ZPM contains 122 α-helices and 114 β-strands across 6 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: 27 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	210-214	5
α-helix	215-217	3
α-helix	226-234	9
α-helix	241-248	8
α-helix	256-257	2
β-strand	258-259	2	1
α-helix	270-272	3
β-strand	275	1	2
α-helix	276	1
β-strand	287	1	3
β-strand	290-294	5	3
α-helix	303-311	9
β-strand	317-324	8	3
α-helix	331-344	14
α-helix	347-350	4
β-strand	353-355	3	4
β-strand	359	1	5
α-helix	360-361	2
α-helix	364-369	6
β-strand	377	1	6
α-helix	381-384	4
β-strand	391-392	2	7
α-helix	396-400	5
β-strand	402	1	2
α-helix	403-404	2
α-helix	406-414	9
β-strand	417	1	8
β-strand	421	1	3
α-helix	429-431	3
α-helix	434-450	17
β-strand	453	1	8
α-helix	454-475	22
β-strand	481	1	5
β-strand	482-490	9	3
β-strand	496-506	11	3
β-strand	517-526	10	3
α-helix	534-537	4
β-strand	541-552	12	3
β-strand	555-571	17	3
α-helix	572-579	8
α-helix	583-603	21
α-helix	608-612	5
β-strand	619-624	6	9
β-strand	627-631	5	9
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	1
α-helix	683-691	9
α-helix	698-714	17

Chain B: 30 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-10	6
α-helix	18-21	4
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	102-113	12
β-strand	118	1	11
α-helix	120-123	4
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	163-173	11
β-strand	178-181	4	13
β-strand	210-213	4	13
α-helix	214-221	8
β-strand	223-224	2	14
β-strand	225-226	2	15
β-strand	242-243	2	15
β-strand	245	1	12
α-helix	246-248	3
α-helix	249-263	15
β-strand	269	1	1
α-helix	276-291	16
β-strand	298-305	8	1
β-strand	306	1	16
α-helix	315-325	11
α-helix	331-337	7
α-helix	339-344	6
β-strand	348-350	3	14
β-strand	355-356	2	17
β-strand	357-358	2	7
β-strand	364	1	6
β-strand	367-368	2	17
α-helix	371-374	4
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	437-442	6	1
β-strand	446-453	8	1
α-helix	456-472	17
β-strand	477	1	16
β-strand	483-486	4	1
β-strand	489-491	3	18
β-strand	496-498	3	18
β-strand	501-502	2	18
α-helix	519-537	19
α-helix	541-559	19
α-helix	573-582	10
α-helix	591-593	3
α-helix	595-597	3
α-helix	608-611	4
α-helix	618-624	7
β-strand	667-668	2	19

Chain C: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	43-52	10
β-strand	57-59	3	19
α-helix	61-65	5
β-strand	70	1	20
β-strand	76	1	20
β-strand	78-82	5	19
β-strand	89-91	3	19
α-helix	94-102	9
α-helix	111-114	4
α-helix	116-119	4

Chain D: 24 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	210-215	6
α-helix	226-234	9
α-helix	241-248	8
α-helix	256-257	2
β-strand	258-259	2	21
β-strand	275	1	22
α-helix	276	1
β-strand	287	1	23
β-strand	290-294	5	23
α-helix	303-311	9
β-strand	317-324	8	23
α-helix	331-344	14
α-helix	347-350	4
β-strand	353-355	3	4
β-strand	359-360	2	24
α-helix	364-369	6
β-strand	377	1	25
α-helix	381-384	4
β-strand	391-392	2	26
β-strand	402	1	22
α-helix	403-404	2
α-helix	406-414	9
β-strand	417	1	27
β-strand	421	1	23
α-helix	425-427	3
α-helix	429-431	3
α-helix	434-450	17
β-strand	453	1	27
α-helix	454-475	22
β-strand	480-481	2	24
β-strand	482-490	9	23
β-strand	496-506	11	23
β-strand	517-526	10	23
α-helix	534-537	4
β-strand	541-552	12	23
β-strand	555-571	17	23
α-helix	572-579	8
α-helix	583-602	20
α-helix	608-612	5
β-strand	619-623	5	28
β-strand	628-631	4	28
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	21
α-helix	683-691	9
α-helix	698-714	17

Chain E: 31 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	28
α-helix	5-10	6
α-helix	18-21	4
α-helix	36-48	13
β-strand	54-57	4	29
β-strand	64-67	4	29
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-115	14
β-strand	118	1	30
α-helix	120-123	4
β-strand	128-130	3	31
β-strand	135-137	3	31
α-helix	139-152	14
α-helix	158-160	3
β-strand	162	1	30
α-helix	163-172	10
α-helix	173-175	3
β-strand	179-182	4	32
β-strand	209-212	4	32
α-helix	214-220	7
β-strand	223-224	2	33
β-strand	225-226	2	34
β-strand	242-243	2	34
β-strand	245	1	31
α-helix	249-264	16
β-strand	269	1	21
α-helix	276-288	13
β-strand	298-306	9	21
α-helix	315-325	11
α-helix	331-337	7
α-helix	340-345	6
β-strand	347-350	4	33
β-strand	355-356	2	35
β-strand	357-358	2	26
β-strand	364	1	25
β-strand	367-368	2	35
α-helix	370-372	3
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	33
β-strand	400-403	4	33
α-helix	413-425	13
α-helix	429-432	4
β-strand	437-442	6	21
β-strand	446-453	8	21
α-helix	456-472	17
β-strand	477-486	10	21
β-strand	489-491	3	36
β-strand	496-498	3	36
β-strand	501-502	2	36
α-helix	519-537	19
α-helix	541-559	19
α-helix	573-582	10
α-helix	591-593	3
α-helix	595-597	3
α-helix	608-611	4
α-helix	618-624	7
β-strand	667-668	2	37

Chain F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	43-51	9
β-strand	57-59	3	37
α-helix	61-65	5
β-strand	70	1	38
β-strand	76	1	38
β-strand	78-82	5	37
β-strand	89-91	3	37
α-helix	94-102	9
α-helix	111-114	4
α-helix	116-119	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A, D	protein	717	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	M9TI86
RNA-directed RNA polymerase catalytic subunit	B, E	protein	757	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	M9TLW3
Polymerase basic protein 2	C, F	protein	759	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	X5F427

Sequence of entity 1 (A, D), FASTA

>7ZPM_1 Polymerase acidic protein (chains A, D)
GMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGE
STIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIE
IGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIR
QEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPN
GCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEG
EGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKN
MKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTD
SSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDD
FQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEK
YCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAE
SSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFS
AESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B, E), FASTA

>7ZPM_2 RNA-directed RNA polymerase catalytic subunit (chains B, E)
MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELKKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Sequence of entity 3 (C, F), FASTA

>7ZPM_3 Polymerase basic protein 2 (chains C, F)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN

Primary citation

Direct observation of backtracking by influenza A and B polymerases upon consecutive incorporation of the nucleoside analog T1106. Kouba, T., Dubankova, A., Drncova, P. et al. Cell Rep (2023) 42:111901-111901. DOI 10.1016/j.celrep.2022.111901 · 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)
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…
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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