4WRT: Influenza B polymerase with bound vRNA promoter

Crystal structure of Influenza B polymerase with bound vRNA promoter (form FluB2). Determined by X-ray diffraction at 2.7 Å resolution. Released 19 Nov 2014.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Influenza B virus
Chains: 5
Atoms: 14,972
Mol. weight: 273.02 kDa
Released: 19 Nov 2014

Explore 4WRT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4WRT contains 100 α-helices and 71 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, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-50	19
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	117-124	8	2
α-helix	128-139	12
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	164-183	20
α-helix	187-191	5
α-helix	206-213	8
α-helix	217	1
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	291-295	5	5
α-helix	302-312	11
α-helix	314-317	4
β-strand	323-326	4	5
α-helix	333-348	16
β-strand	355-356	2	5
α-helix	357	1
α-helix	360-365	6
α-helix	372	1
β-strand	373-374	2	6
α-helix	377-382	6
β-strand	387	1	6
α-helix	389-392	4
α-helix	394-396	3
β-strand	398	1	4
α-helix	401-410	10
β-strand	413	1	7
β-strand	417	1	5
α-helix	425-427	3
α-helix	430-447	18
β-strand	449	1	7
α-helix	450-471	22
β-strand	476-486	11	5
β-strand	492-502	11	5
β-strand	513-522	10	5
α-helix	530-532	3
β-strand	537-545	9	5
β-strand	550-563	14	5
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	8
β-strand	623-628	6	8
α-helix	629-645	17
α-helix	649-669	21
β-strand	675-676	2	3
α-helix	679-687	9
α-helix	694-715	22

Chain B: 44 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
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	9
β-strand	64-67	4	9
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	10
α-helix	119-124	6
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-151	13
α-helix	157-160	4
β-strand	162	1	10
α-helix	163-172	10
α-helix	173-175	3
β-strand	178-192	15	12
β-strand	199-213	15	12
α-helix	214-221	8
β-strand	223-228	6	13
β-strand	240-244	5	13
β-strand	245	1	11
α-helix	246-263	18
β-strand	269	1	3
α-helix	275-291	17
α-helix	294	1
β-strand	298-303	6	3
β-strand	306	1	14
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-345	15
β-strand	348-350	3	13
β-strand	355-359	5	6
β-strand	364-368	5	6
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	13
β-strand	401-403	3	13
α-helix	414-425	12
β-strand	435-442	8	3
β-strand	445-452	8	3
α-helix	455-470	16
β-strand	476	1	14
β-strand	482-485	4	3
β-strand	488-491	4	15
β-strand	494-497	4	15
β-strand	500	1	15
α-helix	501-502	2
α-helix	504-511	8
α-helix	518-535	18
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	600-602	3
α-helix	607-611	5
α-helix	612-614	3
α-helix	617-623	7
α-helix	636-640	5
β-strand	641-642	2	16
β-strand	654-655	2	16
β-strand	667	1	17
α-helix	668-670	3
α-helix	672-675	4
α-helix	680-698	19
β-strand	712	1	18
α-helix	713-730	18
α-helix	736-748	13

Chain C: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	16-24	9
β-strand	26	1	18
α-helix	27-33	7
α-helix	45-52	8
β-strand	59-62	4	17
α-helix	65-68	4
β-strand	73-74	2	19
β-strand	77-78	2	19
β-strand	80-84	5	17
α-helix	85	1
β-strand	89-93	5	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
β-strand	156	1	22
α-helix	158-169	12
α-helix	171-173	3
α-helix	179-183	5
α-helix	185-194	10
α-helix	202-211	10
β-strand	214	1	22
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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Influenza virus polymerase vRNA promoter 3' end	R	RNA	18	Influenza B virus
Influenza virus polymerase vRNA promoter 5' end	V	RNA	14	Influenza B virus
PA	A	protein	751	Influenza B virus	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B	protein	772	Influenza B virus	Q5V8Y6
PB2	C	protein	798	Influenza B virus	Q5V8X3

Sequence of entity 1 (R), FASTA

>4WRT_1 Influenza virus polymerase vRNA promoter 3' end (chains R)
UAUACCUCUGCUUCUGCU

Sequence of entity 2 (V), FASTA

>4WRT_2 Influenza virus polymerase vRNA promoter 5' end (chains V)
AGUAGUAACAAGAG

Sequence of entity 3 (A), FASTA

>4WRT_3 PA (chains A)
GSHHHHHHHHGSGSMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCY
VISDMNFLDEEGKAYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKY
LADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEG
KGRVLSRLTELQAELSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGM
RSYIDNIDPKGAIERNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMS
DELGLANMTEGKSKKPKTLAKECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNT
ISNEEMSNELQKTNYAKWATGDGLTYQKIMKEVAIDDETMCQEEPKIPNKCRVAAWVQTE
MNLLSTLTSKRALDLPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLL
NESNASMGKYKVIPITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDP
RVDSGKWPKYTVFRIGSLFVSGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEA
IVEQESSIQGYDMTKACFKGDRVNSPKTFSIGTQEGKLVKGSFGKALRVIFTKCLMHYVF
GNAQLEGFSAESRRLLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEW
LGFEKEGSKVLESVDEIMDEGSGSGENLYFQ

Sequence of entity 4 (B), FASTA

>4WRT_4 RNA-directed RNA polymerase catalytic subunit (chains B)
GSGSGSGSGMNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSN
KGKQYISDVTGCTMVDPTNGPLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAM
ETLMVTTVDKLTQGRQTFDWTVCRNQPAATALNTTITSFRLNDLNGADKGGLIPFCQDII
DSLDRPEMTFFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDA
ERGKLKRRAIATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLS
NCPPGGISMTVTGDNTKWNECLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARL
GKGFMITSKTKRLKAQIPCPDLFSIPLERYNEETRAKLKKLKPFFNEEGTASLSPGMMMG
MFNMLSTVLGVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKL
LGINMSKKKSYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKN
NMINNGMGPATAQTAIQLFIADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVA
DGGPNIYNLRNLHIPEIVLKYNLMDPEYKGRLLHPQNPFVGHLSIEGIKEADITPAHGPV
KKMDYDAVSGTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQH
SMLEAMAHRLRMDARLDYESGRMSKDDFEKAMAHLGEIGYIGSGSGENLYFQ

Sequence of entity 5 (C), FASTA

>4WRT_5 PB2 (chains C)
GSGSGSGSGMTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKW
AMCSNFPLALTKGDMANRIPLEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTE
GFERVYESFFLRKMRLDNATWGRITFGPVERVRKRVLLNPLTKEMPPDEASNVIMEILFP
KEAGIPRESTWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFI
EMLHCLQGENWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVI
DTEPLKSCLAAIDGGDVACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNG
TIQKIGIWDGEEEFHVRCGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTR
MFQGVRGEINFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNA
SDYTLKGVVVTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMIT
YDTPKMWEMGTTKELVQNTYQWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAG
QYSGFARAVLKQMRDQEVMKTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIE
VRKGSPLFSYNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDF
KTIEELEKLKPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSG
WSHPQFEKGSGSENLYFQ

Primary citation

Structural insight into cap-snatching and RNA synthesis by influenza polymerase. Reich, S., Guilligay, D., Pflug, A. et al. Nature (2014) 516:361-366. DOI 10.1038/nature14009 · 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…
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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