8BEK: Polymerase acidic protein

Early transcription elongation state of influenza A/H7N9 backtracked polymerase with singly incoporated T1106 at the U +1 position. Determined by electron microscopy at 2.86 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 2.86 Å
Organisms: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9)), Influenza A virus
Chains: 6
Atoms: 18,635
Mol. weight: 272.77 kDa
Ligands: MG, GTA
Released: 28 Dec 2022

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

Secondary structure: helices and β-sheets

8BEK contains 111 α-helices and 101 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, 29 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	33-49	17
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	154-156	3	2
α-helix	157-159	3
α-helix	165-184	20
α-helix	188-193	6
α-helix	210-216	7
α-helix	226-234	9
α-helix	241-248	8
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	359-360	2	6
α-helix	361	1
α-helix	364-369	6
α-helix	376	1
β-strand	377-379	3	7
α-helix	381-384	4
β-strand	391-392	2	7
α-helix	396-400	5
β-strand	402	1	4
α-helix	406-414	9
β-strand	417	1	8
β-strand	420-421	2	5
α-helix	425-427	3
α-helix	429-431	3
α-helix	434-451	18
β-strand	453	1	8
α-helix	454-475	22
β-strand	480-481	2	6
β-strand	482-491	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	619-623	5	9
β-strand	628-631	4	9
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: 38 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
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	10
β-strand	64-67	4	10
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	11
α-helix	119-123	5
β-strand	127-130	4	12
β-strand	135-138	4	12
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-174	12
β-strand	178-184	7	13
β-strand	207-213	7	13
α-helix	214-221	8
β-strand	223-224	2	14
β-strand	225-228	4	15
β-strand	240-243	4	15
β-strand	245	1	12
α-helix	246-263	18
β-strand	269	1	3
α-helix	275-292	18
β-strand	298-304	7	3
β-strand	306	1	16
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-344	14
β-strand	348-350	3	14
β-strand	354-359	6	7
β-strand	364-369	6	7
α-helix	370-375	6
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	437-443	7	3
β-strand	446-453	8	3
α-helix	456-472	17
β-strand	477	1	16
β-strand	483-486	4	3
β-strand	489-492	4	17
β-strand	495-498	4	17
β-strand	501	1	17
α-helix	505-508	4
α-helix	509-511	3
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-582	10
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	18
α-helix	673-676	4
α-helix	680-697	18
α-helix	701-703	3
β-strand	713	1	19
α-helix	714-732	19
α-helix	737-755	19

Chain C: 37 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	19
α-helix	25-32	8
α-helix	43-51	9
β-strand	57-59	3	18
α-helix	63-66	4
β-strand	70	1	20
β-strand	76	1	20
β-strand	78-82	5	18
α-helix	83	1
β-strand	89-91	3	18
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	21
β-strand	141-148	8	22
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	22
α-helix	226-230	5
α-helix	232-235	4
β-strand	236	1	21
β-strand	240-245	6	21
α-helix	249-251	3
α-helix	252-271	20
α-helix	276-285	10
β-strand	287-289	3	23
β-strand	292-293	2	23
α-helix	294-300	7
α-helix	306-314	9
β-strand	319	1	24
β-strand	322-325	4	25
β-strand	328-335	8	25
β-strand	339-345	7	26
β-strand	351-357	7	26
β-strand	361-366	6	25
β-strand	371-377	7	25
β-strand	380-386	7	25
α-helix	391-404	14
α-helix	408-412	5
β-strand	421	1	27
β-strand	427	1	27
α-helix	430-440	11
α-helix	443-449	7
β-strand	451-453	3	28
β-strand	461	1	25
β-strand	473-475	3	28
β-strand	478-480	3	25
α-helix	488-490	3
β-strand	494	1	24
β-strand	497-498	2	29
β-strand	504-505	2	29
β-strand	511-513	3	29
α-helix	515-517	3
β-strand	529-531	3	23
α-helix	542-555	14
α-helix	557-566	10
α-helix	568-571	4
α-helix	578-583	6
α-helix	586-605	20
α-helix	612-618	7
α-helix	619-622	4
β-strand	635-640	6	30
β-strand	643-648	6	30
β-strand	656-659	4	31
β-strand	664-667	4	31
β-strand	670-674	5	31
α-helix	675-677	3
β-strand	687	1	32
β-strand	694-699	6	32
α-helix	702-704	3
β-strand	708	1	32
α-helix	710-712	3
β-strand	721-724	4	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
mRNA	M	RNA	17	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

>8BEK_1 Polymerase acidic protein (chains A)
GMEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGE
STIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIE
IGVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIR
QEMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPN
GCIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEG
EGIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIENEEKIPRTKN
MKKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTD
SSWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDD
FQLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEK
YCVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAE
SSVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFS
AESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>8BEK_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

>8BEK_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

>8BEK_4 mRNA (chains M)
AUCUAUAAUAGUUUXUU

Sequence of entity 5 (R), FASTA

>8BEK_5 3' vRNA (chains R)
UAUACCUCUGAAUAAACUAUU

Sequence of entity 6 (V), FASTA

>8BEK_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…
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
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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