7R0E: Polymerase acidic protein

Early transcription elongation state of influenza A/H7N9 polymerase backtracked due to double incoproation of nucleotide analogue T1106 and with singly incoporated T1106 at the +1 position. Determined by electron microscopy at 2.51 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 2.51 Å
Organisms: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)), Influenza A virus
Chains: 6
Atoms: 18,554
Mol. weight: 273.74 kDa
Ligands: MG, GTA
Released: 28 Dec 2022

Explore 7R0E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R0E contains 119 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: 36 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	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	155-156	2	2
α-helix	157-159	3
α-helix	165-183	19
α-helix	188-193	6
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	3
α-helix	270-272	3
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	331-349	19
β-strand	358-360	3	5
α-helix	361	1
α-helix	364-369	6
α-helix	376	1
β-strand	377-379	3	6
α-helix	381-384	4
β-strand	391-392	2	6
α-helix	396-400	5
β-strand	402	1	4
α-helix	406-414	9
β-strand	417	1	7
α-helix	418	1
β-strand	421	1	5
α-helix	429-431	3
α-helix	434-450	17
β-strand	453	1	7
α-helix	454-475	22
β-strand	480-490	11	5
β-strand	496-506	11	5
β-strand	518-526	9	5
α-helix	534-537	4
β-strand	540-551	12	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	619-623	5	8
β-strand	628-631	4	8
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	3
α-helix	683-691	9
α-helix	698-714	17

Chain B: 41 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
α-helix	5-10	6
α-helix	14-21	8
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	119-123	5
β-strand	127-130	4	11
β-strand	135-138	4	11
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	10
α-helix	163-174	12
β-strand	178-185	8	12
β-strand	206-213	8	12
α-helix	214-221	8
β-strand	223-224	2	13
β-strand	225-228	4	14
α-helix	229-230	2
β-strand	240-243	4	14
β-strand	245	1	11
α-helix	249-264	16
β-strand	269	1	3
α-helix	275-292	18
β-strand	298-304	7	3
β-strand	306	1	15
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	13
β-strand	354-359	6	6
β-strand	364-369	6	6
α-helix	370-372	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	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	502-503	2
α-helix	509-511	3
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	601-603	3
α-helix	608-611	4
α-helix	613-615	3
α-helix	618-624	7
β-strand	667-668	2	17
α-helix	669-671	3
α-helix	673-676	4
α-helix	681-697	17
α-helix	701-703	3
β-strand	713	1	18
α-helix	714-732	19
α-helix	737-755	19

Chain C: 42 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	18
α-helix	25-32	8
α-helix	43-50	8
β-strand	57-59	3	17
α-helix	63-66	4
β-strand	70	1	19
β-strand	76	1	19
β-strand	78-82	5	17
α-helix	83	1
α-helix	88	1
β-strand	89-91	3	17
α-helix	93-102	10
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	252-270	19
α-helix	276-285	10
β-strand	287-289	3	22
β-strand	292-293	2	22
α-helix	294-299	6
α-helix	306-314	9
β-strand	319	1	23
β-strand	322-325	4	24
β-strand	328-335	8	24
β-strand	339-345	7	25
β-strand	351-357	7	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	430-438	9
α-helix	443-449	7
β-strand	452-453	2	27
α-helix	460	1
β-strand	461	1	24
α-helix	462	1
β-strand	473-474	2	27
β-strand	478-480	3	24
β-strand	494	1	23
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	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	586-588	3
α-helix	589-605	17
α-helix	612-618	7
α-helix	619-623	5
α-helix	625-626	2
β-strand	635-640	6	29
β-strand	643-648	6	29
β-strand	656-659	4	30
β-strand	664-667	4	30
β-strand	670-674	5	30
β-strand	687	1	31
β-strand	694-698	5	31
α-helix	702-704	3
β-strand	708	1	31
α-helix	710-712	3
β-strand	722-724	3	31
β-strand	732-736	5	31

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
mRNA	M	RNA	20	Influenza A virus
3' vRNA	R	RNA	21	Influenza A virus
5' vRNA	V	RNA	14	Influenza A virus

Sequence of entity 1 (A), FASTA

>7R0E_1 Polymerase acidic protein (chains A)
GMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGE
STIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIE
IGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIR
QEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPN
GCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEG
EGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKN
MKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTD
SSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDD
FQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEK
YCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAE
SSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFS
AESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>7R0E_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

>7R0E_3 Polymerase basic protein 2 (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAIN

Sequence of entity 4 (M), FASTA

>7R0E_4 mRNA (chains M)
AUCUAUAAUAGUUUXUUCXX

Sequence of entity 5 (R), FASTA

>7R0E_5 3' vRNA (chains R)
UAUACCUCUGAAUAAACUAUU

Sequence of entity 6 (V), FASTA

>7R0E_6 5' vRNA (chains V)
AGUAGUAACAAGAG

Ligands and cofactors

ID	Name	Formula	Copies
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…
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…
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 7R0E 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.