7NI0: Polymerase acidic protein

1918 H1N1 Viral influenza polymerase heterotrimer - Replicase (class 3). Determined by electron microscopy at 3.32 Å resolution. Released 1 Dec 2021.

Method: Electron microscopy
Resolution: 3.32 Å
Organisms: Influenza A virus (strain A/Brevig Mission/1/1918 H1N1), Staphylococcus aureus, Influenza A virus (A/Brevig Mission/1/1918(H1N1))
Chains: 5
Atoms: 14,834
Mol. weight: 281.91 kDa
Released: 1 Dec 2021

Explore 7NI0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7NI0 contains 93 α-helices and 79 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: 27 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	210-216	7
α-helix	226-235	10
α-helix	242-248	7
α-helix	256-257	2
β-strand	258-259	2	1
α-helix	265-269	5
β-strand	275	1	2
α-helix	276	1
β-strand	290-291	2	3
α-helix	303-312	10
β-strand	321-324	4	3
α-helix	331-350	20
β-strand	359-360	2	3
α-helix	364-369	6
α-helix	376	1
β-strand	377-379	3	4
α-helix	381-383	3
β-strand	390-392	3	4
α-helix	393-394	2
α-helix	397-400	4
β-strand	402	1	2
α-helix	406-414	9
β-strand	420-421	2	3
α-helix	425-427	3
α-helix	429-431	3
α-helix	434-451	18
α-helix	454-475	22
β-strand	480-491	12	3
β-strand	496-506	11	3
β-strand	517-526	10	3
α-helix	534-537	4
β-strand	541-548	8	3
β-strand	559-571	13	3
α-helix	572-578	7
α-helix	583-600	18
α-helix	608-609	2
α-helix	610-614	5
β-strand	619-623	5	5
β-strand	628-631	4	5
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	1
α-helix	683-690	8
α-helix	698-713	16

Chain B: 41 helices, 29 β-strands

Element	Residues	Length	Sheet
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	6
β-strand	64-67	4	6
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
α-helix	119-123	5
β-strand	127-130	4	7
β-strand	135-138	4	7
α-helix	139-153	15
α-helix	157-160	4
α-helix	163-173	11
β-strand	178-184	7	8
β-strand	207-213	7	8
α-helix	214-222	9
β-strand	223-224	2	9
β-strand	225-228	4	10
β-strand	240-243	4	10
α-helix	246-264	19
β-strand	269	1	1
α-helix	275-287	13
α-helix	288-292	5
β-strand	298-305	8	1
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	9
β-strand	355-359	5	4
β-strand	364-368	5	4
α-helix	370-374	5
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	9
β-strand	400-402	3	9
α-helix	413-425	13
β-strand	437-443	7	1
β-strand	446-453	8	1
α-helix	456-471	16
β-strand	478	1	1
β-strand	484-486	3	1
β-strand	489-492	4	11
β-strand	495-498	4	11
β-strand	501	1	11
α-helix	509-511	3
α-helix	519-535	17
α-helix	541-559	19
α-helix	574-582	9
α-helix	586-588	3
α-helix	591-593	3
α-helix	601-603	3
α-helix	618-624	7
β-strand	632	1	12
α-helix	637-639	3
β-strand	642-645	4	13
α-helix	646-647	2
β-strand	653-656	4	13
β-strand	666	1	12
α-helix	667	1
β-strand	668	1	14
α-helix	669	1
α-helix	673-676	4
α-helix	678-680	3
α-helix	682-699	18
α-helix	701-703	3
β-strand	713	1	15
α-helix	714-731	18
α-helix	737-755	19

Chain C: 25 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	15
α-helix	28-33	6
α-helix	38-40	3
α-helix	43-49	7
α-helix	50-52	3
β-strand	57-59	3	14
α-helix	61-65	5
β-strand	70	1	16
β-strand	76	1	16
β-strand	78-82	5	14
β-strand	89-91	3	14
α-helix	94-102	9
α-helix	110-114	5
α-helix	116-126	11
β-strand	129-135	7	17
β-strand	141-146	6	18
β-strand	154	1	19
α-helix	156-167	12
α-helix	180-192	13
α-helix	200-211	12
β-strand	212	1	19
β-strand	215-220	6	18
α-helix	232-235	4
β-strand	236	1	17
β-strand	240-245	6	17
α-helix	251-272	22
α-helix	276-285	10
β-strand	287-289	3	20
β-strand	292-293	2	20
α-helix	294-300	7
α-helix	306-314	9
β-strand	324-325	2	21
β-strand	328-329	2	21
β-strand	331-334	4	22
β-strand	342-345	4	23
β-strand	351-354	4	23
α-helix	356-358	3
β-strand	361-366	6	22
β-strand	371-377	7	22
β-strand	380-386	7	22
α-helix	391-405	15
α-helix	408-411	4
β-strand	421	1	24
β-strand	427	1	24
α-helix	430-437	8
α-helix	443-447	5
β-strand	452-453	2	25
α-helix	460	1
β-strand	461	1	22
α-helix	462-463	2
β-strand	473-474	2	25
β-strand	478-480	3	22
β-strand	496-498	3	26
β-strand	504-506	3	26
β-strand	511-513	3	26
β-strand	529-531	3	20

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	716	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)	Q3HM39
RNA-directed RNA polymerase catalytic subunit	B	protein	757	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1)	Q3HM40
Polymerase basic protein 2,Immunoglobulin G-binding protein A	C	protein	905	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1), Staphylococcus aureus	P38507 (AlphaFold model)
RNA (5'-r(pgpgpcpcpupgpcpu)-3')	E	RNA	17	Influenza A virus (A/Brevig Mission/1/1918(H1N1))
RNA (5'-r(papgpupapgpapapapcpapapgpgpcp*c)-3')	D	RNA	15	Influenza A virus (A/Brevig Mission/1/1918(H1N1))

Sequence of entity 1 (A), FASTA

>7NI0_1 Polymerase acidic protein (chains A)
MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINERGES
IIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEI
GVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQ
EMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNG
YIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGE
GIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNM
KKTSQLKWALGENMAPEKVDFDDCKDVSDLKQYDSDEPELRSLASWIQSEFNKACELTDS
SWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDF
QLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKY
CVLEIGDMLLRSAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES
SVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSA
ESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>7NI0_2 RNA-directed RNA polymerase catalytic subunit (chains B)
MDVNPTLLFLKVPAQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHQYSEKGRWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEVVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMESMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVETLARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQIPAEMLASIDLKYFNDSTRKKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKRYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLLGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSIGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRSFEIKKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPLNPFVSHKEIESVNNAVMMPAHGPAKNMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Sequence of entity 3 (C), FASTA

>7NI0_3 Polymerase basic protein 2,Immunoglobulin G-binding protein A (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQGQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSAVHYPKIYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKEELQDCKISPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGIRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGRDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSMRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEVN
GPESVLVNTYQWIIRNWETVKIQWSQNPTMLYNKMEFEPFQSLVPKAARGQYSGFVRTLF
QQMRDVLGTFDTVQIIKLLPFAAAPPKQSRMQFSSLTVNVRGSGMRILVRGNSPVFNYNK
ATKRLTVLGKDAGALTEDPDEGTAGVESAVLRGFLILGKEDRRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINENLYFQGELKTAALAQHDEAV
DNKFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKDDPSQSANLLAEAKKLNDAQAPKVDN
KFNKEQQNAFYEILHLPNLNEEQRNAFIQSLKADPSQSANLLAEAKKLNGAQAPKVDANS
AGKST

Sequence of entity 4 (E), FASTA

>7NI0_4 RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') (chains E)
GGCCUGCUUUUGCUAUU

Sequence of entity 5 (D), FASTA

>7NI0_5 RNA (5'-R(P*AP*GP*UP*AP*GP*AP*AP*AP*CP*AP*AP*GP*GP*CP*C)-3') (chains D)
AGUAGAAACAAGGCC

Primary citation

Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies. Keown, J.R., Zhu, Z., Carrique, L. et al. Nat Commun (2022) 13:251-251. DOI 10.1038/s41467-021-27950-w · 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…
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
8R65 4.23 Å, 1918 H1N1 Viral polymerase heterotrimer in complex with 4 repeat serine-5 phosphorylated…
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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