6QCW: Polymerase acidic protein

Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer. Determined by X-ray diffraction at 2.88 Å resolution. Released 5 Jun 2019.

Method: X-ray diffraction
Resolution: 2.88 Å
Organisms: Influenza B virus, synthetic construct
Chains: 6
Atoms: 18,540
Mol. weight: 279.18 kDa
Ligands: PO4
Released: 5 Jun 2019

Explore 6QCW in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6QCW contains 121 α-helices and 100 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: 40 helices, 29 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-48	17
β-strand	52-54	3	1
β-strand	60-62	3	1
β-strand	75	1	1
β-strand	77	1	2
α-helix	85-99	15
α-helix	102-104	3
α-helix	107-108	2
β-strand	110-112	3	2
β-strand	117-124	8	2
α-helix	128-134	7
β-strand	144-149	6	2
β-strand	153-156	4	2
α-helix	164-174	11
α-helix	177-183	7
α-helix	188-191	4
α-helix	206-213	8
α-helix	223-232	10
α-helix	238-245	8
β-strand	255-256	2	3
α-helix	259-261	3
α-helix	263-264	2
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	4
α-helix	277-279	3
β-strand	291-294	4	5
α-helix	302-312	11
α-helix	314-318	5
β-strand	323-326	4	6
α-helix	333-348	16
β-strand	355-356	2	6
α-helix	360-365	6
α-helix	372	1
β-strand	373-374	2	7
α-helix	377-382	6
β-strand	387	1	7
α-helix	388-392	5
α-helix	394-396	3
β-strand	398	1	4
α-helix	401-411	11
β-strand	413	1	8
β-strand	417	1	5
α-helix	425-427	3
α-helix	430-447	18
β-strand	449	1	8
α-helix	450-471	22
β-strand	476-481	6	6
β-strand	484-486	3	5
β-strand	492-496	5	5
β-strand	498-502	5	6
β-strand	513-522	10	6
α-helix	530-532	3
β-strand	537-545	9	6
β-strand	550-563	14	6
α-helix	564-571	8
α-helix	576-595	20
α-helix	600-604	5
α-helix	610-613	4
β-strand	614-620	7	9
β-strand	623-628	6	9
α-helix	629-645	17
α-helix	649-670	22
β-strand	675-676	2	3
α-helix	679-687	9
α-helix	694-713	20
α-helix	715-718	4

Chain B: 42 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-7	3
α-helix	8-11	4
α-helix	18-21	4
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	103-116	14
β-strand	118	1	11
α-helix	120-122	3
β-strand	127-130	4	12
β-strand	135-138	4	12
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-173	11
β-strand	178-192	15	13
β-strand	199-213	15	13
α-helix	214-221	8
β-strand	223-228	6	14
β-strand	240-244	5	14
β-strand	245	1	12
α-helix	246-264	19
β-strand	269	1	3
α-helix	275-291	17
α-helix	294	1
β-strand	298-303	6	3
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	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	3
β-strand	445-452	8	3
α-helix	455-472	18
β-strand	476	1	15
β-strand	482-485	4	3
β-strand	488-491	4	16
β-strand	494-497	4	16
β-strand	500	1	16
α-helix	501-502	2
α-helix	508-511	4
α-helix	518-534	17
α-helix	540-557	18
α-helix	570-581	12
α-helix	585-587	3
α-helix	590-592	3
α-helix	594-596	3
α-helix	607-611	5
α-helix	612-614	3
α-helix	617-623	7
α-helix	648-652	5
β-strand	667	1	17
α-helix	668-670	3
α-helix	672-674	3
α-helix	677-680	4
α-helix	681-698	18
α-helix	701-704	4
β-strand	712	1	18
α-helix	713-731	19
α-helix	736-747	12

Chain C: 39 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	16-24	9
β-strand	26	1	18
α-helix	30-33	4
α-helix	40-41	2
α-helix	45-52	8
β-strand	59-60	2	17
α-helix	67-69	3
β-strand	73	1	19
β-strand	78	1	19
β-strand	80-84	5	17
α-helix	85	1
β-strand	91-93	3	17
α-helix	95-104	10
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-137	7	20
β-strand	143-148	6	21
α-helix	158-169	12
α-helix	177-178	2
α-helix	180-183	4
α-helix	185-194	10
α-helix	202-211	10
β-strand	217-222	6	21
α-helix	228-231	4
α-helix	234-237	4
β-strand	238	1	20
β-strand	242-247	6	20
α-helix	254-272	19
α-helix	278-288	11
β-strand	289-291	3	22
β-strand	294-295	2	22
α-helix	296-302	7
α-helix	308-317	10
β-strand	324-327	4	23
β-strand	330-333	4	23
β-strand	334-336	3	24
β-strand	340-348	9	25
β-strand	352-360	9	25
β-strand	363-365	3	24
β-strand	368-369	2	26
β-strand	372-373	2	26
β-strand	374-379	6	24
β-strand	382-388	7	24
α-helix	393-407	15
α-helix	410-414	5
β-strand	423	1	27
β-strand	429	1	27
α-helix	432-442	11
α-helix	444-449	6
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	24
β-strand	497-499	3	30
β-strand	504-507	4	30
β-strand	512-515	4	30
α-helix	516-518	3
α-helix	529	1
β-strand	530-532	3	22
α-helix	538-540	3
α-helix	543-556	14
α-helix	558-567	10
α-helix	576-582	7
α-helix	587-607	21
α-helix	612-618	7
α-helix	619-621	3
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	691-693	3
β-strand	699-702	4	33
α-helix	714-718	5
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	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B	protein	772	Influenza B virus	Q5V8Y6
Polymerase basic protein 2	C	protein	798	Influenza B virus	Q5V8X3
RNA (5'-d((gdm))-r(pgpapapupgpcpcpapupapapupap*g)-3')	M	RNA	15	synthetic construct
RNA (5'-r(upapupapcpcpupcpupgpcpupupcpupgpcpupapup*u)-3')	R	RNA	21	synthetic construct
RNA (5'-r(papgpupapgpupapapcpapapgpapg)-3')	V	RNA	14	synthetic construct

Sequence of entity 1 (A), FASTA

>6QCW_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

>6QCW_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

>6QCW_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 (M), FASTA

>6QCW_4 RNA (5'-D(*(GDM))-R(P*GP*AP*AP*UP*GP*CP*CP*AP*UP*AP*AP*UP*AP*G)-3') (chains M)
XGAAUGCUAUAAUAG

Sequence of entity 5 (R), FASTA

>6QCW_5 RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*UP*CP*UP*GP*CP*UP*AP*UP*U)-3') (chains R)
UAUACCUCUGCUUCUGCUAUU

Sequence of entity 6 (V), FASTA

>6QCW_6 RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*G)-3') (chains V)
AGUAGUAACAAGAG

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3

Primary citation

Structural snapshots of actively transcribing influenza polymerase. Kouba, T., Drncova, P., Cusack, S. Nat Struct Mol Biol (2019) 26:460-470. DOI 10.1038/s41594-019-0232-z · 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
7R1F 2.58 Å, Early transcription elongation state of influenza B polymerase backtracked due to double…
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…

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