8RMP: Influenza polymerase A/H7N9-4M (ENDO(R) | Core1)

Influenza polymerase A/H7N9-4M (ENDO(R) | Core1). Determined by electron microscopy at 2.77 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.77 Å
Organism: Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))
Chains: 3
Atoms: 13,818
Mol. weight: 258.32 kDa
Ligands: MG
Released: 11 Sept 2024

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

Secondary structure: helices and β-sheets

8RMP contains 89 α-helices and 73 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: 35 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-23	13
α-helix	32-49	18
β-strand	53-54	2	1
β-strand	60-61	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	127-137	11
β-strand	143-149	7	2
β-strand	154-156	3	2
α-helix	157-159	3
α-helix	165-184	20
α-helix	188-193	6
β-strand	195-196	2	3
β-strand	199-200	2	3
α-helix	210-216	7
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	4
α-helix	270-272	3
β-strand	275	1	5
α-helix	276	1
β-strand	287	1	6
β-strand	290-292	3	6
α-helix	303-312	10
β-strand	317-324	8	6
α-helix	331-351	21
β-strand	358-360	3	6
α-helix	361-362	2
α-helix	364-369	6
α-helix	376	1
β-strand	377-380	4	7
α-helix	381-384	4
β-strand	390-392	3	7
α-helix	397-400	4
β-strand	402	1	5
α-helix	405-414	10
β-strand	417	1	8
β-strand	421	1	6
α-helix	429-431	3
α-helix	434-450	17
β-strand	453	1	8
α-helix	454-475	22
β-strand	480-490	11	6
β-strand	496-506	11	6
α-helix	516	1
β-strand	517-526	10	6
α-helix	530-532	3
α-helix	534-537	4
β-strand	541-552	12	6
β-strand	555-571	17	6
α-helix	572-579	8
α-helix	583-603	21
α-helix	608-612	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	4
α-helix	683-691	9
α-helix	698-715	18

Chain B: 34 helices, 27 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-10	6
α-helix	18-21	4
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
α-helix	119-124	6
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-152	14
α-helix	157-160	4
α-helix	163-174	12
β-strand	178-182	5	12
β-strand	209-213	5	12
α-helix	214-221	8
β-strand	223-225	3	13
β-strand	243-244	2	13
β-strand	245	1	11
α-helix	246-264	19
β-strand	269	1	4
α-helix	276-291	16
β-strand	298-306	9	4
α-helix	315-325	11
α-helix	331-344	14
β-strand	348-350	3	13
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	13
β-strand	400-402	3	13
α-helix	413-425	13
α-helix	429-432	4
β-strand	437-443	7	4
β-strand	446-453	8	4
α-helix	456-473	18
β-strand	477-486	10	4
β-strand	489-492	4	14
β-strand	495-498	4	14
β-strand	501-504	4	14
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	608-611	4
α-helix	618-624	7
α-helix	637-639	3
β-strand	642-644	3	15
β-strand	654-656	3	15
β-strand	667-668	2	16
α-helix	669-670	2
α-helix	688-693	6
α-helix	702-705	4
β-strand	713	1	17
α-helix	714-732	19
α-helix	737-755	19

Chain C: 20 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	17
α-helix	28-32	5
α-helix	39-40	2
α-helix	43-51	9
β-strand	57-58	2	16
α-helix	61-65	5
β-strand	70	1	18
β-strand	76	1	18
β-strand	78-79	2	16
β-strand	90-91	2	16
α-helix	93-102	10
α-helix	104-105	2
α-helix	110-114	5
α-helix	116-126	11
β-strand	129-135	7	19
α-helix	140	1
β-strand	141-146	6	20
β-strand	154	1	21
α-helix	156-167	12
α-helix	169-171	3
α-helix	174-178	5
α-helix	184-192	9
α-helix	200-211	12
β-strand	212	1	21
β-strand	215-220	6	20
α-helix	226-228	3
α-helix	232-235	4
β-strand	236	1	19
β-strand	240-245	6	19
β-strand	694-699	6	22
α-helix	702-704	3
β-strand	708	1	22
α-helix	710-715	6
β-strand	721-726	6	22
β-strand	730-736	7	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	716	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))	S5ME50
Polymerase basic protein 2	C	protein	788	Influenza A virus (A/Zhejiang/DTID-ZJU01/2013(H7N9))	X5F427

Sequence of entity 1 (A), FASTA

>8RMP_1 Polymerase acidic protein (chains A)
MEDFVRQCFNPMIVELAEKAMKEYGEDPKIETNKFASICTHLEVCFMYSDFHFIDERGES
TIIESGDPNVLLKHRFEIIEGRDRTMAWTVVNSICNTTGVEKPKFLPDLYDYKENRFIEI
GVTRREVHIYYLEKANKIKSEKTHIHIFSFTGEEMATKADYTLDEESRARIKTRLFTIRQ
EMASRGLWDSFRQSERGEETIEERFEITGTMRRLADQSLPPNFSSLENFRAYVDGFEPNG
CIEGKLSQMSKEVNARIEPFLRTTPRPLRLPDGPPCSQRSKFLLMDALKLSIEDPSHEGE
GIPLYDAIKCMKTFFGWKEPNIIKPHEKGINPNYLLTWKQVLAELQDIKNEEKIPRTKNM
KKTSQLKWALGENMAPEKVDFEDCKDVNDLKQYDSDEPEPRSLACWIQSEFNKACELTDS
SWVELDEIGEDVAPIEHIASMRRNYFTAEVSHCRATEYIMKGVYINTALLNASCAAMDDF
QLIPMISKCITKEGRRKTNLYGFIIKGRSHLRNDTDVVNFVSMEFSLTDPRLEPHKWEKY
CVLEIGDMLLRTAVGQVSRPMFLYVRTNGTSKIKMKWGMEMRRCLLQSLQQIESMIEAES
SVKEKDLTKEFFENKSETWPIGESPKGVEEGSIGKVCRTLLAKSVFNSLYASPQLEGFSA
ESRKLLLIVQALRDNLEPGTFDLEGLYEAIEECLINDPWVLLNASWFNSFLTHALR

Sequence of entity 2 (B), FASTA

>8RMP_2 RNA-directed RNA polymerase catalytic subunit (chains B)
MDVNPTLLFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVNRTHKYSEKGKWTTNTE
TGAPQLNPIDGPLPEDNEPSGYAQTDCVLEAMAFLEESHPGIFENSCLETMEIVQQTRVD
KLTQGRQTYDWTLNRNQPAATALANTIEVFRSNGLTANESGRLIDFLKDVMDSMDKEEME
ITTHFQRKRRVRDNMTKKMVTQRTIGKKKQRLNKRSYLIRALTLNTMTKDAERGKLKRRA
IATPGMQIRGFVYFVEALARSICEKLEQSGLPVGGNEKKAKLANVVRKMMTNSQDTELSF
TITGDNTKWNENQNPRMFLAMITYITRNQPEWFRNVLSIAPIMFSNKMARLGKGYMFESK
SMKLRTQVPAEMLANIDLKYFNKSTREKIEKIRPLLIDGTASLSPGMMMGMFNMLSTVLG
VSILNLGQKKYTKTTYWWDGLQSSDDFALIVNAPNHEGIQAGVDRFYRTCKLVGINMSKK
KSYINRTGTFEFTSFFYRYGFVANFSMELPSFGVSGINESADMSVGVTVIKNNMINNDLG
PATAQMALQLFIKDYRYTYRCHRGDTQIQTRRAFELGKLWEQTRSKAGLLVSDGGPNLYN
IRNLHIPEVCLKWELMDEDYQGRLCNPMNPFVSHKEIDSVNNAVVMPAHGPAKSMEYDAV
ATTHSWIPKRNRSILNTSQRGILEDEQMYQKCCNLFEKFFPSSSYRRPVGISSMVEAMVS
RARIDARIDFESGRIKKEEFAEIMKICSTIEELRRQK

Sequence of entity 3 (C), FASTA

>8RMP_3 Polymerase basic protein 2 (chains C)
MERIKELRDLMSQSRTREILTKTTVDHMAIIKKYTSGRQEKNPALRMKWMMAMKYPITAD
KRIMEMIPERNEQRQTLWSKTNDAGSDRVMVSPLAVTWWNRNGPTTSTVHYPKVYKTYFE
KVERLKHGTFGPVHFRNQVKIRRRVDINPGHADLSAKEAQDVIMEVVFPNEVGARILTSE
SQLTITKEKKKELQDCKIAPLMVAYMLERELVRKTRFLPVAGGTSSVYIEVLHLTQGTCW
EQMYTPGGEVRNDDVDQSLIIAARNIVRRATVSADPLASLLEMCHSTQIGGVRMVDILRQ
NPTEEQAVDICKAAMGLRISSSFSFGGFTFKRTSGSSVKREEEVLTGNLQTLKIRVHEGY
EEFTMVGRRATAILRKATRRLIQLIVSGKDEQSIAEAIIVAMVFSQEDCMIKAVRGDLNF
VNRANQRLNPMHQLLRHFQKDAKVLFQNWGIEPIDNVMGMIGILPDMTPSTEMSLRGVRV
SKMGVDEYSSTERVVVSIDRFLRVRDQRGNVLLSPEEVSETQGTEKLTITYSSSMMWEIN
GPESVLVNTYQWIIRNWENVKIQWSQDPTMLYNKMEFEPFQSLVPKAARGQYSGFVRVLF
QQMRDVLGTFDTVQIIKLLPFAAAPPEQSRMQFSSLTVNVRGSGMRIVVRGNSPVFNYNK
ATKRLTVLGKDAGALMEDPDEGTAGVESAVLRGFLILGKENKRYGPALSINELSNLAKGE
KANVLIGQGDVVLVMKRKRDSSILTDSQTATKRIRMAINGWSHPQFEKGGGSGGGSGGSA
WSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	1

Primary citation

Structures of influenza A and B replication complexes give insight into avian to human host adaptation and reveal a role of ANP32 as an electrostatic chaperone for the apo-polymerase. Arragain, B., Krischuns, T., Pelosse, M. et al. Nat Commun (2024) 15:6910-6910. DOI 10.1038/s41467-024-51007-3 · 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)
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

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