7ZPL: Symmetric dimer of influenza A/H7N9 polymerase

Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook. Determined by electron microscopy at 3.12 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 3.12 Å
Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Chains: 8
Atoms: 19,919
Mol. weight: 520.01 kDa
Ligands: MG
Released: 28 Dec 2022

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

Secondary structure: helices and β-sheets

7ZPL contains 114 α-helices and 110 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.

Chains A and D: 22 helices, 22 β-strands

Element	Residues	Length	Sheet
α-helix	209-216	8
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	1
β-strand	275	1	2
α-helix	276	1
β-strand	287	1	3
β-strand	290-292	3	3
α-helix	303-312	10
β-strand	317-324	8	3
α-helix	331-349	19
β-strand	353-355	3	4
β-strand	359-360	2	5
α-helix	364-369	6
α-helix	376	1
β-strand	377-378	2	6
α-helix	382-384	3
β-strand	390-392	3	6
α-helix	396-400	5
β-strand	402	1	2
α-helix	406-414	9
β-strand	417	1	7
β-strand	421	1	3
α-helix	429-431	3
α-helix	434-450	17
β-strand	453	1	7
α-helix	454-475	22
β-strand	480-481	2	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	572-578	7
α-helix	583-601	19
α-helix	609-612	4
β-strand	619-623	5	8
β-strand	628-631	4	8
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	1
α-helix	683-692	10
α-helix	698-713	16

Chain B: 30 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
α-helix	5-10	6
α-helix	18-21	4
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	102-115	14
β-strand	118	1	10
α-helix	120-122	3
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-152	14
β-strand	162	1	10
α-helix	163-173	11
β-strand	178-179	2	12
β-strand	212-213	2	12
α-helix	214-221	8
β-strand	223-224	2	13
β-strand	225-228	4	14
β-strand	240-243	4	14
α-helix	249-264	16
β-strand	269	1	1
α-helix	275-290	16
β-strand	298-305	8	1
β-strand	306	1	15
α-helix	310-312	3
α-helix	315-325	11
α-helix	331-344	14
β-strand	348-350	3	13
β-strand	354-359	6	6
β-strand	364-369	6	6
α-helix	370-374	5
α-helix	383-392	10
β-strand	396-397	2	13
β-strand	400-402	3	13
α-helix	414-425	12
α-helix	429-432	4
β-strand	437-442	6	1
β-strand	446-453	8	1
α-helix	456-473	18
β-strand	477	1	15
β-strand	483-486	4	1
β-strand	489-492	4	16
β-strand	495-498	4	16
β-strand	501-504	4	16
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	601-603	3
α-helix	608-611	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	667-668	2	17

Chains C and F: 5 helices, 5 β-strands

Element	Residues	Length	Sheet
α-helix	43-51	9
β-strand	57-59	3	17
α-helix	63-66	4
β-strand	70	1	18
β-strand	76	1	18
β-strand	78-82	5	17
α-helix	83	1
β-strand	89-91	3	17
α-helix	93-101	9
α-helix	111-114	4

Chain E: 30 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	25
α-helix	5-10	6
α-helix	18-21	4
α-helix	27-29	3
α-helix	36-48	13
β-strand	54-57	4	26
β-strand	64-67	4	26
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-115	14
β-strand	118	1	27
α-helix	120-122	3
β-strand	128-130	3	28
β-strand	135-137	3	28
α-helix	139-152	14
β-strand	162	1	27
α-helix	163-173	11
β-strand	178-179	2	29
β-strand	212-213	2	29
α-helix	214-221	8
β-strand	223-224	2	30
β-strand	225-228	4	31
β-strand	240-243	4	31
α-helix	249-264	16
β-strand	269	1	19
α-helix	275-290	16
β-strand	298-305	8	19
β-strand	306	1	32
α-helix	310-312	3
α-helix	315-325	11
α-helix	331-344	14
β-strand	348-350	3	30
β-strand	354-359	6	23
β-strand	364-369	6	23
α-helix	370-374	5
α-helix	383-392	10
β-strand	396-397	2	30
β-strand	400-402	3	30
α-helix	414-425	12
α-helix	429-432	4
β-strand	437-442	6	19
β-strand	446-453	8	19
α-helix	456-473	18
β-strand	477	1	32
β-strand	483-486	4	19
β-strand	489-492	4	33
β-strand	495-498	4	33
β-strand	501-504	4	33
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	601-603	3
α-helix	608-611	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	668	1	34

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
5' vRNA	U, V	RNA	14	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))

Sequence of entity 1 (A, D), FASTA

>7ZPL_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

>7ZPL_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

>7ZPL_3 Polymerase basic protein 2 (chains C, F)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN

Sequence of entity 4 (U, V), FASTA

>7ZPL_4 5' vRNA (chains U, V)
AGUAGUAACAAGAG

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

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)
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…
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

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