7QTL: Influenza A/H7N9 polymerase elongation complex

Influenza A/H7N9 polymerase elongation complex. Determined by electron microscopy at 2.48 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 2.48 Å
Organisms: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)), Influenza A virus
Chains: 6
Atoms: 18,397
Mol. weight: 273.29 kDa
Ligands: 2TM, MG, GTA
Released: 28 Dec 2022

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

Secondary structure: helices and β-sheets

7QTL contains 114 α-helices and 100 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: 37 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-49	18
β-strand	53-54	2	1
β-strand	60-61	2	1
β-strand	74	1	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	157-159	3
α-helix	165-184	20
α-helix	188-192	5
α-helix	210-216	7
α-helix	226-235	10
α-helix	241-248	8
α-helix	256-257	2
β-strand	258-259	2	3
α-helix	265-268	4
β-strand	275	1	4
α-helix	276	1
β-strand	287	1	5
β-strand	290-292	3	5
α-helix	303-312	10
β-strand	317-324	8	5
α-helix	331-351	21
β-strand	358-359	2	5
α-helix	360-361	2
α-helix	364-369	6
α-helix	376	1
β-strand	377-378	2	6
α-helix	381-384	4
β-strand	391-392	2	6
α-helix	393-394	2
α-helix	396-400	5
β-strand	402	1	4
α-helix	406-414	9
β-strand	417	1	7
β-strand	421	1	5
α-helix	429-431	3
α-helix	434-451	18
β-strand	453	1	7
α-helix	454-475	22
β-strand	481-490	10	5
β-strand	496-506	11	5
α-helix	516-517	2
β-strand	518-526	9	5
α-helix	534-537	4
β-strand	541-551	11	5
β-strand	556-570	15	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: 39 helices, 30 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	36-49	14
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	157-160	4
β-strand	162	1	10
α-helix	163-173	11
β-strand	178-182	5	12
β-strand	209-213	5	12
α-helix	214-221	8
β-strand	223-228	6	13
α-helix	229-230	2
β-strand	240-244	5	13
α-helix	246-264	19
β-strand	269	1	3
α-helix	275-292	18
β-strand	298-304	7	3
β-strand	306	1	14
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	13
β-strand	355-359	5	6
β-strand	364-368	5	6
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	13
β-strand	400-402	3	13
α-helix	413-425	13
α-helix	429-432	4
β-strand	437-443	7	3
β-strand	446-453	8	3
α-helix	456-472	17
β-strand	477	1	14
β-strand	483-486	4	3
β-strand	489-492	4	15
β-strand	495-498	4	15
β-strand	501	1	15
α-helix	502-503	2
α-helix	506-511	6
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	608-611	4
α-helix	618-624	7
β-strand	636	1	16
β-strand	656	1	16
α-helix	657-659	3
β-strand	667-668	2	17
α-helix	679-681	3
α-helix	682-699	18
β-strand	713	1	18
α-helix	714-732	19
α-helix	737-755	19

Chain C: 38 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	15-21	7
β-strand	24	1	18
α-helix	25-33	9
α-helix	43-50	8
β-strand	57-60	4	17
α-helix	61-65	5
β-strand	70	1	19
β-strand	76	1	19
β-strand	78-79	2	17
β-strand	88-91	4	17
α-helix	93-102	10
α-helix	104-105	2
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	20
β-strand	141-148	8	21
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-192	13
α-helix	200-211	12
β-strand	214-220	7	21
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	20
β-strand	240-245	6	20
α-helix	249-251	3
α-helix	252-272	21
α-helix	276-285	10
β-strand	287-289	3	22
β-strand	292-293	2	22
α-helix	294-298	5
α-helix	306-314	9
β-strand	319	1	23
β-strand	323-325	3	24
β-strand	328-335	8	24
β-strand	338-345	8	25
β-strand	351-358	8	25
β-strand	361-366	6	24
β-strand	371-377	7	24
β-strand	380-386	7	24
α-helix	391-405	15
α-helix	408-412	5
β-strand	421	1	26
α-helix	426	1
β-strand	427	1	26
α-helix	428-429	2
α-helix	430-440	11
α-helix	443-449	7
β-strand	451-453	3	27
β-strand	462-463	2	28
β-strand	469-470	2	28
β-strand	473-475	3	27
β-strand	478-480	3	24
β-strand	494	1	23
β-strand	504-505	2	29
β-strand	511-513	3	29
α-helix	515-517	3
β-strand	529-531	3	22
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	586-605	20
α-helix	612-618	7
α-helix	620-623	4
α-helix	625-628	4
β-strand	635-640	6	30
β-strand	643-648	6	30
β-strand	657-658	2	31
β-strand	664-667	4	31
β-strand	670-674	5	31
β-strand	687-691	5	32
β-strand	694-699	6	32
α-helix	702-704	3
β-strand	708	1	32
α-helix	710-712	3
β-strand	720-724	5	32
β-strand	732-736	5	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	717	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	759	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	X5F427
5' vRNA	V	RNA	14	Influenza A virus
3' vRNA	R	RNA	21	Influenza A virus
mRNA	M	RNA	17	Influenza A virus

Sequence of entity 1 (A), FASTA

>7QTL_1 Polymerase acidic protein (chains A)
GMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGE
STIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIE
IGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIR
QEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPN
GCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEG
EGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKN
MKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTD
SSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDD
FQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEK
YCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAE
SSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFS
AESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>7QTL_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

>7QTL_3 Polymerase basic protein 2 (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN

Sequence of entity 4 (V), FASTA

>7QTL_4 5' vRNA (chains V)
AGUAGUAACAAGAG

Sequence of entity 5 (R), FASTA

>7QTL_5 3' vRNA (chains R)
UAUACCUCUGCUUCUGCUAUU

Sequence of entity 6 (M), FASTA

>7QTL_6 mRNA (chains M)
AUCUAUAAUAGCAGAAG

Ligands and cofactors

ID	Name	Formula	Copies
2TM	5'-O-[(S)-hydroxy{[(S)-hydroxy(phosphonooxy)phosphoryl]methyl}phosphoryl]cytidi…	C10 H18 N3 O13 P3	1
MG	Magnesium ion	Mg	2
GTA	P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate	C21 H30 N10 O17 P3	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…
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
7ZPL 3.12 Å, Symmetric dimer of influenza A/H7N9 polymerase bound to 5' vRNA hook

Browse structure collections

About this viewer

MolViewer shows 7QTL directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.