7R1F: Polymerase acidic protein

Early transcription elongation state of influenza B polymerase backtracked due to double incoproation of nucleotide analogue T1106. Determined by electron microscopy at 2.58 Å resolution. Released 28 Dec 2022.

Method: Electron microscopy
Resolution: 2.58 Å
Organisms: Influenza B virus (B/Memphis/13/2003), Influenza B virus
Chains: 6
Atoms: 18,372
Mol. weight: 281.28 kDa
Ligands: GTA, MG
Released: 28 Dec 2022

Explore 7R1F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7R1F contains 122 α-helices and 99 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: 39 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-23	13
α-helix	32-49	18
β-strand	52-54	3	1
β-strand	60-62	3	1
β-strand	75	1	1
β-strand	77-79	3	2
α-helix	85-98	14
α-helix	102-104	3
β-strand	110-112	3	2
β-strand	117-119	3	2
β-strand	121-124	4	3
α-helix	128-139	12
β-strand	146-149	4	3
β-strand	154-155	2	3
α-helix	164-183	20
α-helix	187-191	5
α-helix	206-214	9
α-helix	217	1
α-helix	223-232	10
α-helix	238-245	8
β-strand	255-256	2	4
α-helix	259-261	3
α-helix	263-264	2
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	5
α-helix	277-279	3
β-strand	291-294	4	6
α-helix	302-312	11
α-helix	314-317	4
β-strand	324-326	3	6
α-helix	333-348	16
β-strand	355-356	2	6
α-helix	360-366	7
α-helix	372	1
β-strand	373-374	2	7
α-helix	377-382	6
β-strand	387-388	2	7
α-helix	389-392	4
α-helix	394-396	3
β-strand	398	1	5
α-helix	401-410	10
β-strand	413	1	8
β-strand	417	1	6
α-helix	425-427	3
α-helix	430-447	18
β-strand	449	1	8
α-helix	450-471	22
β-strand	476-486	11	6
β-strand	492-502	11	6
β-strand	514-522	9	6
α-helix	530-532	3
β-strand	537-545	9	6
β-strand	550-562	13	6
α-helix	564-571	8
α-helix	573-575	3
α-helix	576-595	20
α-helix	600-604	5
α-helix	611-613	3
β-strand	614-620	7	9
β-strand	624-628	5	9
α-helix	629-645	17
α-helix	649-669	21
β-strand	675-676	2	4
α-helix	679-687	9
α-helix	694-714	21

Chain B: 41 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	1-3	3	9
α-helix	5-7	3
α-helix	8-11	4
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	102-115	14
β-strand	118	1	11
α-helix	119-123	5
β-strand	128-130	3	12
β-strand	135-137	3	12
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-173	11
β-strand	178-191	14	13
β-strand	200-213	14	13
α-helix	214-221	8
β-strand	223-228	6	14
β-strand	240-244	5	14
α-helix	246-264	19
β-strand	269	1	4
α-helix	275-291	17
α-helix	294	1
β-strand	298-304	7	4
β-strand	306	1	15
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	14
β-strand	355-359	5	7
β-strand	364-368	5	7
α-helix	370-372	3
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396-397	2	14
β-strand	401-403	3	14
α-helix	414-425	12
β-strand	435-442	8	4
β-strand	445-452	8	4
α-helix	455-471	17
β-strand	476	1	15
β-strand	482-485	4	4
β-strand	488-491	4	16
β-strand	494-497	4	16
β-strand	500	1	16
α-helix	501-502	2
α-helix	505-511	7
α-helix	518-535	18
α-helix	540-558	19
α-helix	570-581	12
α-helix	585-587	3
α-helix	590-592	3
α-helix	594-596	3
α-helix	607-610	4
α-helix	617-623	7
α-helix	632-634	3
α-helix	655-656	2
β-strand	657	1	17
α-helix	658	1
β-strand	676	1	13
α-helix	681-698	18
β-strand	712	1	18
α-helix	713-730	18
α-helix	736-748	13

Chain C: 42 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	16-24	9
β-strand	26	1	18
α-helix	30-33	4
α-helix	40-42	3
α-helix	45-52	8
β-strand	59-60	2	19
α-helix	61-63	3
α-helix	65-68	4
β-strand	73-74	2	20
β-strand	77-78	2	20
β-strand	80	1	19
α-helix	83-85	3
β-strand	92-93	2	19
α-helix	95-104	10
α-helix	106-107	2
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-137	7	21
β-strand	143-148	6	22
β-strand	156	1	23
α-helix	158-169	12
α-helix	179-183	5
α-helix	185-194	10
β-strand	200	1	17
α-helix	202-213	12
β-strand	214	1	23
β-strand	217-222	6	22
α-helix	228-231	4
α-helix	234-237	4
β-strand	238	1	21
β-strand	242-247	6	21
α-helix	254-272	19
α-helix	278-287	10
β-strand	289-291	3	24
β-strand	294-295	2	24
α-helix	296-302	7
α-helix	308-317	10
β-strand	324-326	3	25
β-strand	331-336	6	25
β-strand	341-347	7	26
β-strand	353-359	7	26
β-strand	363-369	7	25
β-strand	372-379	8	25
β-strand	382-388	7	25
α-helix	393-406	14
α-helix	410-414	5
β-strand	423	1	27
β-strand	429	1	27
α-helix	432-442	11
α-helix	444-451	8
β-strand	454-455	2	28
α-helix	456-457	2
β-strand	465	1	29
β-strand	471	1	29
β-strand	474-475	2	28
β-strand	479-481	3	25
β-strand	498-499	2	30
β-strand	505-506	2	30
β-strand	512-514	3	30
α-helix	516-518	3
β-strand	530-532	3	24
α-helix	537-540	4
α-helix	543-556	14
α-helix	558-567	10
α-helix	571-573	3
α-helix	576-582	7
α-helix	590-606	17
α-helix	612-618	7
α-helix	625-626	2
α-helix	633-635	3
β-strand	639-641	3	31
β-strand	649-651	3	31
β-strand	659-662	4	32
β-strand	667-670	4	32
β-strand	673-676	4	32
α-helix	683-687	5
α-helix	690-693	4
β-strand	699-702	4	33
α-helix	711-712	2
α-helix	714-718	5
α-helix	720-721	2
β-strand	725-729	5	33
β-strand	735-739	5	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	751	Influenza B virus (B/Memphis/13/2003)	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B	protein	772	Influenza B virus (B/Memphis/13/2003)	Q5V8Y6
Polymerase basic protein 2	C	protein	798	Influenza B virus (B/Memphis/13/2003)	Q5V8X3
5' vRNA	V	RNA	14	Influenza B virus
3' vRNA	R	RNA	21	Influenza B virus
mRNA	M	RNA	20	Influenza B virus

Sequence of entity 1 (A), FASTA

>7R1F_1 Polymerase acidic protein (chains A)
GSHHHHHHHHGSGSMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCY
VISDMNFLDEEGKAYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKY
LADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEG
KGRVLSRLTELQAELSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGM
RSYIDNIDPKGAIERNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMS
DELGLANMTEGKSKKPKTLAKECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNT
ISNEEMSNELQKTNYAKWATGDGLTYQKIMKEVAIDDETMCQEEPKIPNKCRVAAWVQTE
MNLLSTLTSKRALDLPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLL
NESNASMGKYKVIPITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDP
RVDSGKWPKYTVFRIGSLFVSGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEA
IVEQESSIQGYDMTKACFKGDRVNSPKTFSIGTQEGKLVKGSFGKALRVIFTKCLMHYVF
GNAQLEGFSAESRRLLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEW
LGFEKEGSKVLESVDEIMDEGSGSGENLYFQ

Sequence of entity 2 (B), FASTA

>7R1F_2 RNA-directed RNA polymerase catalytic subunit (chains B)
GSGSGSGSGMNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSN
KGKQYISDVTGCTMVDPTNGPLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAM
ETLMVTTVDKLTQGRQTFDWTVCRNQPAATALNTTITSFRLNDLNGADKGGLIPFCQDII
DSLDRPEMTFFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDA
ERGKLKRRAIATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLS
NCPPGGISMTVTGDNTKWNECLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARL
GKGFMITSKTKRLKAQIPCPDLFSIPLERYNEETRAKLKKLKPFFNEEGTASLSPGMMMG
MFNMLSTVLGVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKL
LGINMSKKKSYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKN
NMINNGMGPATAQTAIQLFIADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVA
DGGPNIYNLRNLHIPEIVLKYNLMDPEYKGRLLHPQNPFVGHLSIEGIKEADITPAHGPV
KKMDYDAVSGTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQH
SMLEAMAHRLRMDARLDYESGRMSKDDFEKAMAHLGEIGYIGSGSGENLYFQ

Sequence of entity 3 (C), FASTA

>7R1F_3 Polymerase basic protein 2 (chains C)
GSGSGSGSGMTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKW
AMCSNFPLALTKGDMANRIPLEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTE
GFERVYESFFLRKMRLDNATWGRITFGPVERVRKRVLLNPLTKEMPPDEASNVIMEILFP
KEAGIPRESTWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFI
EMLHCLQGENWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVI
DTEPLKSCLAAIDGGDVACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNG
TIQKIGIWDGEEEFHVRCGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTR
MFQGVRGEINFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNA
SDYTLKGVVVTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMIT
YDTPKMWEMGTTKELVQNTYQWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAG
QYSGFARAVLKQMRDQEVMKTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIE
VRKGSPLFSYNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDF
KTIEELEKLKPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSG
WSHPQFEKGSGSENLYFQ

Sequence of entity 4 (V), FASTA

>7R1F_4 5' vRNA (chains V)
AGUAGUAACAAGAG

Sequence of entity 5 (R), FASTA

>7R1F_5 3' vRNA (chains R)
UAUACAACUGAGAAAGCUAUU

Sequence of entity 6 (M), FASTA

>7R1F_6 mRNA (chains M)
AUCUAUAAUAGCUUUCUCXX

Ligands and cofactors

ID	Name	Formula	Copies
GTA	P1-7-methylguanosine-P3-adenosine-5',5'-triphosphate	C21 H30 N10 O17 P3	1
MG	Magnesium ion	Mg	3

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 Q5V8Z9), best resolution first:

5FML 1.7 Å, Crystal structure of the endonuclease from the PA subunit of influenza B virus bound to…
6FS8 1.8 Å, Influenza B/Memphis/13/03 endonuclease with bound inhibitor, baloxavir acid (BXA)
6FSB 1.8 Å, Influenza B/Memphis/13/03 endonuclease with I38T mutation
6FS9 2.28 Å, Influenza B/Memphis/13/03 endonuclease with I38T mutation with bound inhibitor,…
8BE0 2.34 Å, Early transcription elongation state of influenza B/Mem polymerase backtracked due to…
7Z42 2.42 Å, Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B
4WRT 2.7 Å, Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2)
8BDR 2.7 Å, Early transcription elongation state of influenza B/Mem polymerase backtracked due to…
8RN3 2.78 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza…
8RN6 2.82 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B…
8RN4 2.87 Å, Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B…
6QCW 2.88 Å, Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

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