8R65: 1918 H1N1 Viral polymerase heterotrimer

1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated PolII peptide with ordered PB2 C-terminal domains. Determined by electron microscopy at 4.23 Å resolution. Released 27 Mar 2024.

Method: Electron microscopy
Resolution: 4.23 Å
Organisms: Influenza A virus (A/Brevig Mission/1/1918(H1N1)), Homo sapiens
Chains: 6
Atoms: 18,079
Mol. weight: 285.08 kDa
Released: 27 Mar 2024

Explore 8R65 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8R65 contains 109 α-helices and 106 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: 31 helices, 34 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-24	14
α-helix	32-49	18
β-strand	53	1	1
β-strand	54	1	2
β-strand	60	1	2
β-strand	74	1	1
β-strand	76	1	3
α-helix	84-98	15
α-helix	101-103	3
β-strand	109-111	3	3
β-strand	116-123	8	3
α-helix	127-137	11
β-strand	144-149	6	3
β-strand	154-156	3	3
α-helix	165-185	21
α-helix	188-193	6
α-helix	210-215	6
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	4
β-strand	275	1	5
α-helix	276	1
β-strand	292-293	2	6
α-helix	303-311	9
β-strand	317-322	6	7
α-helix	332-350	19
α-helix	359	1
β-strand	360	1	8
α-helix	361	1
α-helix	364-369	6
α-helix	376	1
β-strand	377-379	3	9
β-strand	391-392	2	9
α-helix	397-400	4
β-strand	402	1	5
α-helix	403-404	2
α-helix	406-413	8
β-strand	417	1	10
α-helix	429-431	3
α-helix	434-451	18
β-strand	453	1	10
α-helix	454-475	22
β-strand	480	1	8
β-strand	483-484	2	7
β-strand	487-490	4	6
β-strand	496-499	4	6
β-strand	502-506	5	7
β-strand	518-519	2	11
β-strand	520-526	7	7
β-strand	543-547	5	7
β-strand	551	1	12
β-strand	556	1	12
β-strand	560-566	7	7
β-strand	569-570	2	11
α-helix	572-579	8
α-helix	583-602	20
α-helix	608-612	5
β-strand	619-624	6	13
β-strand	627-631	5	13
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	4
α-helix	683-693	11
α-helix	698-713	16

Chain B: 40 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2	1	13
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	30
β-strand	64-67	4	30
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	31
α-helix	119-123	5
β-strand	128-130	3	32
β-strand	135-137	3	32
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	31
α-helix	163-174	12
β-strand	178-181	4	33
β-strand	184	1	34
β-strand	207	1	34
β-strand	210-213	4	33
α-helix	214-222	9
β-strand	223-228	6	35
β-strand	240-244	5	35
α-helix	249-264	16
β-strand	269	1	36
α-helix	275-286	12
α-helix	287-291	5
α-helix	292	1
β-strand	298-302	5	36
β-strand	306	1	37
α-helix	310-312	3
α-helix	315-325	11
α-helix	331-344	14
β-strand	348-350	3	35
β-strand	356-359	4	9
β-strand	364-367	4	9
α-helix	370-373	4
α-helix	385-392	8
α-helix	393-395	3
β-strand	396-397	2	35
β-strand	400-402	3	35
α-helix	413-425	13
β-strand	437-443	7	36
β-strand	446-453	8	36
α-helix	456-472	17
β-strand	477	1	37
β-strand	483	1	4
β-strand	484-486	3	36
β-strand	490	1	38
β-strand	497	1	38
β-strand	501	1	38
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	595-597	3
α-helix	608-611	4
α-helix	618-624	7
α-helix	663-665	3
β-strand	667-668	2	15
α-helix	673-676	4
α-helix	681-699	19
α-helix	701-703	3
α-helix	707-709	3
β-strand	713	1	14
α-helix	714-731	18
α-helix	737-755	19

Chain C: 38 helices, 41 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	14
α-helix	28-33	6
α-helix	38-40	3
α-helix	43-50	8
β-strand	57-59	3	15
α-helix	63-66	4
β-strand	70	1	16
β-strand	76	1	16
β-strand	78-82	5	15
α-helix	88	1
β-strand	89-91	3	15
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	17
β-strand	143-146	4	18
α-helix	156-167	12
α-helix	170-172	3
α-helix	180-192	13
α-helix	200-211	12
β-strand	215-218	4	18
α-helix	226-230	5
β-strand	236	1	17
β-strand	240-245	6	17
α-helix	252-272	21
α-helix	276-284	9
β-strand	288-289	2	19
β-strand	292-293	2	19
α-helix	294-300	7
α-helix	306-314	9
β-strand	324-325	2	20
β-strand	328-329	2	20
β-strand	331-334	4	21
β-strand	339	1	22
β-strand	342-345	4	23
β-strand	351-354	4	23
α-helix	356	1
β-strand	357	1	22
α-helix	358	1
β-strand	361-366	6	21
β-strand	371-377	7	21
β-strand	380-386	7	21
α-helix	391-405	15
α-helix	408-411	4
β-strand	421	1	24
α-helix	426	1
β-strand	427	1	24
α-helix	428-429	2
α-helix	430-437	8
α-helix	443-449	7
β-strand	452-453	2	25
α-helix	457-459	3
α-helix	460-463	4
β-strand	473-474	2	25
β-strand	478	1	21
β-strand	497	1	26
β-strand	504-505	2	26
β-strand	511-513	3	26
β-strand	529-530	2	19
α-helix	545-555	11
α-helix	557-563	7
α-helix	569-572	4
α-helix	578-581	4
α-helix	589-605	17
α-helix	612-618	7
α-helix	619-621	3
α-helix	625-626	2
β-strand	635-639	5	27
β-strand	644-648	5	27
β-strand	656-658	3	28
β-strand	664-667	4	28
β-strand	670-674	5	28
β-strand	694-699	6	29
β-strand	708	1	29
α-helix	710-712	3
β-strand	722-726	5	29
β-strand	730-736	7	29

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	716	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q3HM39
Polymerase basic protein 2	C	protein	905	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q3HM41
RNA (5'-r(papgpupapgpapapapcpapapgpgpcp*c)-3')	D	RNA	15	Influenza A virus (A/Brevig Mission/1/1918(H1N1))
RNA (5'-r(pgpgpcpcpupgpcpu)-3')	E	RNA	17	Influenza A virus (A/Brevig Mission/1/1918(H1N1))
RNA polymerase II 4 repeat peptide with serine5 phosphorylation	X	protein	28	Homo sapiens	P24928 (AlphaFold model)
RNA-directed RNA polymerase catalytic subunit	B	protein	757	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q3HM40

Sequence of entity 1 (A), FASTA

>8R65_1 Polymerase acidic protein (chains A)
MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINERGES
IIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPALYDYKENRFIEI
GVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQ
EMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNG
YIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGE
GIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNM
KKTSQLKWALGENMAPEKVDFDDCKDVSDLKQYDSDEPELRSLASWIQSEFNKACELTDS
SWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDF
QLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKY
CVLEIGDMLLRSAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES
SVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSA
ESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (C), FASTA

>8R65_2 Polymerase basic protein 2 (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSAVHYPKIYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKEELQDCKISPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSMRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEVN
GPESVLVNTYQWIIRNWETVKIQWSQNPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLF
QQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNK
ATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDRRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINENLYFQGELKTAALAQHDEAV
DNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDN
KFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKADPSQSANLLAEAKKLNGAQAPKVDANS
AGKST

Sequence of entity 3 (D), FASTA

>8R65_3 RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') (chains D)
AGUAGAAACAAGGCC

Sequence of entity 4 (E), FASTA

>8R65_4 RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') (chains E)
GGCCUGCUUUUGCUAUU

Sequence of entity 5 (X), FASTA

>8R65_5 RNA polymerase II 4 repeat peptide with serine5 phosphorylation (chains X)
YSPTSPSYSPTSPSYSPTSPSYSPTSPS

Sequence of entity 6 (B), FASTA

>8R65_6 RNA-directed RNA polymerase catalytic subunit (chains B)
MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGRWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQIPAEMLASIDLKYFNDSTRKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLLGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFEIKKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESVNNAVMMPAHGPAKNMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Primary citation

Structural and functional characterization of the interaction between the influenza A virus RNA polymerase and the CTD of host RNA polymerase II. Keown, J., Baazaoui, A., Sebesta, M. et al. J Virol (2024) 98:e0013824-e0013824. DOI 10.1128/jvi.00138-24 · PubMed

Other PDB entries of the same protein (UniProt Q3HM39), best resolution first:

9RVE 2.53 Å, Structure of human 1918 influenza A polymerase heterotrimer in complex with 1918 NEP.
7NHC 2.87 Å, 1918 H1N1 Viral influenza polymerase heterotrimer - Endonuclease ordered (Class2b)
7NHA 2.91 Å, 1918 H1N1 Viral influenza polymerase heterotrimer - Endonuclease and priming loop…
9RYC 2.93 Å, Structure of human 1918 influenza A polymerase heterotrimer in complex with WSN NEP.
7NHX 3.23 Å, 1918 H1N1 Viral influenza polymerase heterotrimer - full transcriptase (Class1)
8R60 3.23 Å, 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated…
7NI0 3.32 Å, 1918 H1N1 Viral influenza polymerase heterotrimer - Replicase (class 3)
7NKA 4.07 Å, 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8206
7NK1 4.22 Å, 1918 Influenza virus polymerase heterotirmer in complex with vRNA promoters and Nb8201
7NKC 4.46 Å, 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8207
7NJ3 4.48 Å, 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8196 core
7NJ5 4.63 Å, 1918 H1N1 Viral influenza polymerase heterotrimer with Nb8199 core

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