7Z42: Polymerase acidic protein

Influenza B polymerase with Pol II pSer5 CTD peptide mimic bound in site 2B. Determined by X-ray diffraction at 2.42 Å resolution. Released 18 May 2022.

Method: X-ray diffraction
Resolution: 2.42 Å
Organisms: Influenza B virus, Homo sapiens
Chains: 12
Atoms: 35,949
Mol. weight: 547.04 kDa
Released: 18 May 2022

Explore 7Z42 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7Z42 contains 262 α-helices and 202 β-strands across 8 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	32-49	18
β-strand	52-54	3	1
β-strand	60-62	3	1
β-strand	65	1	2
β-strand	67	1	2
β-strand	75	1	1
β-strand	77	1	3
α-helix	85-98	14
β-strand	110-112	3	3
β-strand	117-124	8	3
α-helix	128-139	12
β-strand	143-149	7	3
β-strand	154-156	3	3
α-helix	159-161	3
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	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	314-318	5
β-strand	323-326	4	6
α-helix	333-347	15
β-strand	355-356	2	6
α-helix	357	1
α-helix	360-366	7
α-helix	372	1
β-strand	373-374	2	7
α-helix	377-382	6
β-strand	387	1	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	564-570	7
α-helix	573-575	3
α-helix	576-595	20
α-helix	600-605	6
α-helix	611-613	3
β-strand	614-620	7	9
β-strand	623-628	6	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: 46 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	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	102-116	15
β-strand	118	1	11
α-helix	119-124	6
β-strand	127-130	4	12
β-strand	135-138	4	12
α-helix	139-151	13
α-helix	157-160	4
β-strand	162	1	11
α-helix	163-172	10
α-helix	173-175	3
β-strand	178-192	15	13
β-strand	199-213	15	13
α-helix	214-221	8
β-strand	223-224	2	14
β-strand	225-228	4	15
α-helix	229-230	2
β-strand	240-243	4	15
β-strand	245	1	12
α-helix	249-264	16
β-strand	269	1	4
α-helix	275-291	17
α-helix	294	1
β-strand	298-305	8	4
β-strand	306	1	16
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-337	7
α-helix	339-345	7
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	1	14
β-strand	401-403	3	14
α-helix	414-427	14
β-strand	435-442	8	4
β-strand	445-452	8	4
α-helix	455-470	16
β-strand	476	1	16
β-strand	482-485	4	4
β-strand	488-491	4	17
β-strand	494-497	4	17
β-strand	500	1	17
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	641-644	4	18
β-strand	652-655	4	18
β-strand	667	1	19
α-helix	668-669	2
β-strand	676	1	13
α-helix	679-698	20
α-helix	706-707	2
β-strand	712	1	20
α-helix	713-729	17
α-helix	736-752	17

Chain C: 44 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	16-24	9
β-strand	26	1	20
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	21
β-strand	77-78	2	21
β-strand	80	1	19
β-strand	92-93	2	19
α-helix	95-104	10
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-136	6	22
β-strand	143-148	6	23
α-helix	158-169	12
α-helix	171-173	3
α-helix	180-183	4
α-helix	185-194	10
α-helix	202-213	12
β-strand	217-222	6	23
α-helix	228-231	4
α-helix	234-237	4
β-strand	238	1	22
β-strand	243-247	5	22
α-helix	254-272	19
α-helix	278-288	11
β-strand	289-291	3	24
β-strand	294-295	2	24
α-helix	296-302	7
α-helix	308-317	10
α-helix	319-322	4
β-strand	324-327	4	25
β-strand	330-336	7	25
β-strand	340-348	9	26
β-strand	352-360	9	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	410-413	4
α-helix	432-442	11
β-strand	453-454	2	27
α-helix	455-457	3
β-strand	463	1	25
β-strand	465	1	28
β-strand	471	1	28
β-strand	475-476	2	27
β-strand	480-481	2	25
β-strand	498-499	2	29
β-strand	505-506	2	29
β-strand	512-514	3	29
α-helix	516-518	3
β-strand	530-532	3	24
α-helix	537-540	4
α-helix	543-556	14
α-helix	558-566	9
α-helix	571-574	4
α-helix	576-578	3
α-helix	579-582	4
α-helix	590-606	17
α-helix	612-618	7
α-helix	619-622	4
α-helix	625-626	2
α-helix	634-636	3
β-strand	639-641	3	30
α-helix	642	1
β-strand	649-651	3	30
β-strand	659-662	4	31
β-strand	667-670	4	31
β-strand	673-676	4	31
α-helix	683-685	3
α-helix	690-693	4
β-strand	699-702	4	32
α-helix	706-708	3
α-helix	711-713	3
α-helix	714-718	5
β-strand	725-729	5	32
β-strand	735-739	5	32

Chain D: 40 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	1-8	8
α-helix	11-23	13
α-helix	32-49	18
β-strand	53-54	2	33
β-strand	60	1	33
β-strand	74-75	2	33
β-strand	77-79	3	34
α-helix	85-98	14
β-strand	110-112	3	34
β-strand	117-124	8	34
α-helix	128-139	12
β-strand	144-149	6	34
β-strand	154-156	3	34
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	35
α-helix	259-261	3
α-helix	263-264	2
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	36
α-helix	277-279	3
β-strand	291-294	4	37
α-helix	302-312	11
α-helix	314-318	5
α-helix	322	1
β-strand	323-326	4	37
α-helix	333-347	15
β-strand	355-356	2	37
α-helix	357	1
α-helix	360-366	7
α-helix	372	1
β-strand	373-374	2	38
α-helix	377-382	6
β-strand	387	1	38
α-helix	389-392	4
α-helix	394-396	3
β-strand	398	1	36
α-helix	401-410	10
β-strand	413	1	39
β-strand	417	1	37
α-helix	425-427	3
α-helix	430-447	18
β-strand	449	1	39
α-helix	450-471	22
β-strand	476-486	11	37
β-strand	492-502	11	37
β-strand	514-522	9	37
α-helix	530-532	3
β-strand	537-545	9	37
β-strand	550-562	13	37
α-helix	564-570	7
α-helix	573-575	3
α-helix	576-595	20
α-helix	600-605	6
α-helix	611-613	3
β-strand	614-620	7	40
β-strand	623-628	6	40
α-helix	629-645	17
α-helix	649-669	21
β-strand	675-676	2	35
α-helix	679-687	9
α-helix	694-714	21

Chain E: 46 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	40
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	41
β-strand	64-67	4	41
α-helix	72-74	3
α-helix	85-98	14
α-helix	102-116	15
β-strand	118	1	42
α-helix	119-124	6
β-strand	127-130	4	43
β-strand	135-138	4	43
α-helix	139-151	13
α-helix	157-160	4
β-strand	162	1	42
α-helix	163-172	10
α-helix	173-175	3
β-strand	178-189	12	44
β-strand	202-213	12	44
α-helix	214-221	8
β-strand	223-224	2	45
β-strand	225-228	4	46
α-helix	229-230	2
β-strand	240-243	4	46
β-strand	245	1	43
α-helix	249-264	16
β-strand	269	1	35
α-helix	275-291	17
α-helix	294	1
β-strand	298-305	8	35
β-strand	306	1	47
α-helix	309-312	4
α-helix	315-325	11
α-helix	331-337	7
α-helix	339-345	7
β-strand	348-350	3	45
β-strand	355-359	5	38
β-strand	364-368	5	38
α-helix	370-372	3
α-helix	378-380	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396	1	45
β-strand	401-403	3	45
α-helix	414-427	14
β-strand	435-442	8	35
β-strand	445-452	8	35
α-helix	455-470	16
β-strand	476	1	47
β-strand	482-485	4	35
β-strand	488-491	4	48
β-strand	494-497	4	48
β-strand	500	1	48
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	641-644	4	49
β-strand	652-655	4	49
β-strand	667	1	50
α-helix	668-669	2
β-strand	676	1	44
α-helix	679-698	20
α-helix	706-707	2
β-strand	712	1	51
α-helix	713-729	17
α-helix	736-752	17

Chain F: 44 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	2-14	13
α-helix	16-24	9
β-strand	26	1	51
α-helix	30-33	4
α-helix	40-42	3
α-helix	45-52	8
β-strand	59-60	2	50
α-helix	61-63	3
α-helix	65-68	4
β-strand	73-74	2	52
β-strand	77-78	2	52
β-strand	80	1	50
β-strand	92-93	2	50
α-helix	95-104	10
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-136	6	53
β-strand	143-148	6	54
α-helix	158-169	12
α-helix	171-173	3
α-helix	180-183	4
α-helix	185-194	10
α-helix	202-213	12
β-strand	217-222	6	54
α-helix	228-231	4
α-helix	234-237	4
β-strand	238	1	53
β-strand	243-247	5	53
α-helix	254-272	19
α-helix	278-288	11
β-strand	289-291	3	55
β-strand	294-295	2	55
α-helix	296-302	7
α-helix	308-317	10
α-helix	319-322	4
β-strand	324-327	4	56
β-strand	330-336	7	56
β-strand	340-348	9	57
β-strand	352-360	9	57
β-strand	363-369	7	56
β-strand	372-379	8	56
β-strand	382-389	8	56
α-helix	393-406	14
α-helix	410-413	4
β-strand	423-424	2	58
β-strand	428-429	2	58
α-helix	432-442	11
β-strand	453-454	2	59
α-helix	455-457	3
β-strand	463	1	56
β-strand	465	1	60
β-strand	471	1	60
β-strand	475-476	2	59
β-strand	479-482	4	56
β-strand	498-499	2	61
β-strand	505-506	2	61
β-strand	512-514	3	61
α-helix	516-518	3
β-strand	530-532	3	55
α-helix	537-540	4
α-helix	543-556	14
α-helix	558-566	9
α-helix	571-574	4
α-helix	576-578	3
α-helix	579-582	4
α-helix	590-606	17
α-helix	612-618	7
α-helix	619-622	4
α-helix	625-626	2
β-strand	628	1	62
β-strand	634	1	62
α-helix	635-636	2
β-strand	639-641	3	63
α-helix	642	1
β-strand	649-651	3	63
β-strand	659-662	4	64
β-strand	667-670	4	64
β-strand	673-676	4	64
α-helix	683-685	3
α-helix	690-693	4
β-strand	699-702	4	65
α-helix	706-708	3
α-helix	711-713	3
α-helix	714-718	5
β-strand	725-729	5	65
β-strand	735-739	5	65

Chains G and I: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A, D	protein	751	Influenza B virus	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B, E	protein	772	Influenza B virus	Q5V8Y6
Polymerase basic protein 2	C, F	protein	798	Influenza B virus	Q5V8X3
DNA-directed RNA polymerase II subunit RPB1	G, I, X, Y	protein	28	Homo sapiens	P24928 (AlphaFold model)
RNA (5'-r(papgpupapgpupapapcpapapgp*a)-3')	H, V	RNA	13	Influenza B virus

Sequence of entity 1 (A, D), FASTA

>7Z42_1 Polymerase acidic protein (chains A, D)
GSHHHHHHHHGSGSMDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCY
VISDMNFLDEEGKAYTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKY
LADLFDYKTKRFIEVGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEG
KGRVLSRLTELQAELSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGM
RSYIDNIDPKGAIERNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMS
DELGLANMTEGKSKKPKTLAKECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNT
ISNEEMSNELQKTNYAKWATGDGLTYQKIMKEVAIDDETMCQEEPKIPNKCRVAAWVQTE
MNLLSTLTSKRALDLPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLL
NESNASMGKYKVIPITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDP
RVDSGKWPKYTVFRIGSLFVSGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEA
IVEQESSIQGYDMTKACFKGDRVNSPKTFSIGTQEGKLVKGSFGKALRVIFTKCLMHYVF
GNAQLEGFSAESRRLLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEW
LGFEKEGSKVLESVDEIMDEGSGSGENLYFQ

Sequence of entity 2 (B, E), FASTA

>7Z42_2 RNA-directed RNA polymerase catalytic subunit (chains B, E)
GSGSGSGSGMNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSN
KGKQYISDVTGCTMVDPTNGPLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAM
ETLMVTTVDKLTQGRQTFDWTVCRNQPAATALNTTITSFRLNDLNGADKGGLIPFCQDII
DSLDRPEMTFFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDA
ERGKLKRRAIATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLS
NCPPGGISMTVTGDNTKWNECLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARL
GKGFMITSKTKRLKAQIPCPDLFSIPLERYNEETRAKLKKLKPFFNEEGTASLSPGMMMG
MFNMLSTVLGVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKL
LGINMSKKKSYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKN
NMINNGMGPATAQTAIQLFIADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVA
DGGPNIYNLRNLHIPEIVLKYNLMDPEYKGRLLHPQNPFVGHLSIEGIKEADITPAHGPV
KKMDYDAVSGTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQH
SMLEAMAHRLRMDARLDYESGRMSKDDFEKAMAHLGEIGYIGSGSGENLYFQ

Sequence of entity 3 (C, F), FASTA

>7Z42_3 Polymerase basic protein 2 (chains C, F)
GSGSGSGSGMTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKW
AMCSNFPLALTKGDMANRIPLEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTE
GFERVYESFFLRKMRLDNATWGRITFGPVERVRKRVLLNPLTKEMPPDEASNVIMEILFP
KEAGIPRESTWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFI
EMLHCLQGENWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVI
DTEPLKSCLAAIDGGDVACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNG
TIQKIGIWDGEEEFHVRCGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTR
MFQGVRGEINFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNA
SDYTLKGVVVTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMIT
YDTPKMWEMGTTKELVQNTYQWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAG
QYSGFARAVLKQMRDQEVMKTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIE
VRKGSPLFSYNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDF
KTIEELEKLKPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSG
WSHPQFEKGSGSENLYFQ

Sequence of entity 4 (G, I, X, Y), FASTA

>7Z42_4 DNA-directed RNA polymerase II subunit RPB1 (chains G, I, X, Y)
YSPTSPSYSPTSPSYSPTSPSYSPTSPS

Sequence of entity 5 (H, V), FASTA

>7Z42_5 RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*A)-3') (chains H, V)
AGUAGUAACAAGA

Primary citation

Type B and type A influenza polymerases have evolved distinct binding interfaces to recruit the RNA polymerase II CTD. Krischuns, T., Isel, C., Drncova, P. et al. PLoS Pathog (2022) 18:e1010328-e1010328. DOI 10.1371/journal.ppat.1010328 · 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…
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…
6QCW 2.88 Å, Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

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