7NKA: Polymerase acidic protein

1918 H1N1 Viral influenza polymerase heterotrimer with Nb8206. Determined by electron microscopy at 4.07 Å resolution. Released 1 Dec 2021.

Method: Electron microscopy
Resolution: 4.07 Å
Organisms: Influenza A virus (A/Brevig Mission/1/1918(H1N1)), Influenza A virus (strain A/Brevig Mission/1/1918 H1N1), synthetic construct
Chains: 6
Atoms: 14,910
Mol. weight: 296.11 kDa
Released: 1 Dec 2021

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

Secondary structure: helices and β-sheets

7NKA contains 87 α-helices and 83 β-strands across 4 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: 34 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	2-7	6
α-helix	11-23	13
α-helix	33-49	17
β-strand	53	1	1
β-strand	61	1	1
β-strand	74	1	1
β-strand	76-78	3	2
α-helix	84-98	15
α-helix	101-103	3
β-strand	109-111	3	2
β-strand	116-120	5	2
β-strand	123	1	3
α-helix	127-137	11
β-strand	144-148	5	2
β-strand	149	1	3
β-strand	154-156	3	2
α-helix	157-159	3
α-helix	165-185	21
α-helix	188-191	4
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	4
α-helix	267-271	5
β-strand	275	1	5
α-helix	276	1
β-strand	290-291	2	6
α-helix	303-312	10
β-strand	317-324	8	6
α-helix	331-350	20
β-strand	358-359	2	6
α-helix	360-361	2
α-helix	364-369	6
α-helix	376	1
β-strand	377-378	2	7
α-helix	381-383	3
β-strand	391-392	2	7
α-helix	397-400	4
β-strand	402	1	5
α-helix	406-414	9
β-strand	420-421	2	6
α-helix	429-431	3
α-helix	434-451	18
α-helix	454-475	22
β-strand	481-491	11	6
β-strand	496-506	11	6
β-strand	517-526	10	6
α-helix	534-537	4
β-strand	540-548	9	6
β-strand	551	1	8
β-strand	556	1	8
β-strand	559-571	13	6
α-helix	572-578	7
α-helix	583-600	18
α-helix	608-613	6
β-strand	619-624	6	9
β-strand	627-631	5	9
α-helix	633-649	17
α-helix	653-673	21
β-strand	679-680	2	4
α-helix	683-691	9
α-helix	698-713	16

Chain B: 37 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	128-130	3	12
β-strand	135-137	3	12
α-helix	139-153	15
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-173	11
β-strand	178-183	6	13
β-strand	208-213	6	13
α-helix	214-221	8
β-strand	223-224	2	14
β-strand	225-228	4	15
β-strand	240-243	4	15
α-helix	249-263	15
β-strand	269	1	4
α-helix	275-292	18
β-strand	298-305	8	4
α-helix	310-312	3
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	14
β-strand	354-359	6	7
β-strand	364-369	6	7
α-helix	370-374	5
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
β-strand	437-443	7	4
β-strand	446-453	8	4
α-helix	456-471	16
β-strand	478	1	4
β-strand	483-486	4	4
β-strand	489-492	4	16
β-strand	495-498	4	16
β-strand	501-502	2	16
α-helix	509-512	4
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	642-645	4	17
β-strand	653-656	4	17
β-strand	668	1	18
α-helix	673-676	4
α-helix	681-699	19
α-helix	701-703	3
β-strand	713	1	19
α-helix	714-731	18
α-helix	737-755	19

Chain C: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	19
α-helix	28-33	6
α-helix	38-40	3
α-helix	43-50	8
β-strand	57-59	3	18
α-helix	61-65	5
β-strand	70	1	20
β-strand	76	1	20
β-strand	78-82	5	18
β-strand	89-91	3	18
α-helix	94-99	6
α-helix	108-110	3
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	21
β-strand	141-146	6	22
β-strand	154	1	23
α-helix	156-167	12
α-helix	180-192	13
α-helix	200-211	12
β-strand	212	1	23
β-strand	215-220	6	22
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	21
β-strand	240-245	6	21

Chain F: 1 helix, 11 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	24
β-strand	10-11	2	25
β-strand	18-24	7	24
β-strand	35-39	5	25
β-strand	46-50	5	25
β-strand	58-59	2	25
β-strand	67-72	6	24
β-strand	77-82	6	24
α-helix	87-89	3
β-strand	91-96	6	25
β-strand	110	1	25
β-strand	114-117	4	25

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
RNA-directed RNA polymerase catalytic subunit	B	protein	757	Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q3HM40
Polymerase basic protein 2,Polymerase basic protein 2	C	protein	905	Influenza A virus (strain A/Brevig Mission/1/1918 H1N1), Influenza A virus (A/Brevig Mission/1/1918(H1N1))	Q3HM41
RNA (5'-r(pgpgpcpcpupgpcpu)-3')	E	RNA	17	synthetic construct
RNA (5'-r(papgpupapgpapapapcpapapgpgpcp*c)-3')	D	RNA	15	synthetic construct
NB8206	F	protein	130	Camelidae mixed library

Sequence of entity 1 (A), FASTA

>7NKA_1 Polymerase acidic protein (chains A)
MEDFVRQCFNPMIVELAEKAMKEYGEDLKIETNKFAAICTHLEVCFMYSDFHFINERGES
IIVESGDPNALLKHRFEIIEGRDRTMAWTVVNSICNTTGAEKPKFLPDLYDYKENRFIEI
GVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQ
EMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNG
YIEGKLSQMSKEVNARIEPFLKTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGE
GIPLYDAIKCMRTFFGWKEPNVVKPHEKGINPNYLLAWKQVLAELQDIENEEKIPKTKNM
KKTSQLKWALGENMAPEKVDFDDCKDVSDLKQYDSDEPELRSLASWIQSEFNKACELTDS
SWIELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDF
QLIPMISKCRTKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKY
CVLEIGDMLLRSAIGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES
SVKEKDMTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSA
ESRKLLLIVQALRDNLEPGTFDLGGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>7NKA_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

>7NKA_3 Polymerase basic protein 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 4 (E), FASTA

>7NKA_4 RNA (5'-R(P*GP*GP*CP*CP*UP*GP*CP*U)-3') (chains E)
GGCCUGCUUUUGCUAUU

Sequence of entity 5 (D), FASTA

>7NKA_5 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 6 (F), FASTA

>7NKA_6 NB8206 (chains F)
QVQLQESGGGLVQPGGSLRLSCTASGGIFGISAMGWYRQAPGKERELVARITRSGSTNFA
DSVKDRFTISRDATENTVVLQMNSLKAEDTAVYYCNGQFWEVDNGNIDLWGQGTQVTVSS
HHHHHHEPEA

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…
7NI0 3.32 Å, 1918 H1N1 Viral influenza polymerase heterotrimer - Replicase (class 3)
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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