8RN2: Polymerase acidic protein

Monomeric apo-influenza B polymerase, encapsidase conformation. Determined by electron microscopy at 2.89 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.89 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 3
Atoms: 15,504
Mol. weight: 258.54 kDa
Released: 11 Sept 2024

Explore 8RN2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RN2 contains 101 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: 36 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-24	14
α-helix	28-30	3
α-helix	32-51	20
β-strand	53	1	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	131-139	9
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	164-183	20
α-helix	193-197	5
α-helix	206-213	8
α-helix	223-232	10
α-helix	238-244	7
β-strand	255-256	2	3
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	4
α-helix	277	1
β-strand	288	1	5
β-strand	291-295	5	5
α-helix	302-312	11
α-helix	314-317	4
β-strand	324-326	3	5
α-helix	333-347	15
β-strand	355	1	5
α-helix	359-365	7
β-strand	373-374	2	6
α-helix	377-382	6
β-strand	387	1	6
α-helix	388-391	4
α-helix	393-395	3
β-strand	398	1	4
α-helix	401-410	10
β-strand	413	1	7
β-strand	416-417	2	5
α-helix	425-427	3
α-helix	430-446	17
β-strand	449	1	7
α-helix	450-471	22
β-strand	477-487	11	5
β-strand	492-502	11	5
β-strand	514-522	9	5
α-helix	530-532	3
β-strand	537-545	9	5
β-strand	550-562	13	5
α-helix	564-572	9
α-helix	573-575	3
α-helix	576-594	19
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	649-670	22
β-strand	675-676	2	3
α-helix	679-687	9
α-helix	694-715	22

Chain B: 30 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
α-helix	5-7	3
α-helix	8-11	4
α-helix	14-17	4
β-strand	22	1	9
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	119-121	3
β-strand	128-130	3	12
β-strand	135-137	3	12
α-helix	139-152	14
β-strand	162	1	11
α-helix	163-173	11
β-strand	178-188	11	13
β-strand	203-213	11	13
α-helix	214-221	8
β-strand	223-226	4	14
β-strand	242-244	3	14
α-helix	246-264	19
β-strand	269	1	3
α-helix	277-291	15
α-helix	294	1
β-strand	298-305	8	3
β-strand	306	1	15
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	356-359	4	6
β-strand	364-367	4	6
α-helix	370-372	3
α-helix	383-392	10
α-helix	393-395	3
β-strand	396	1	14
β-strand	401-403	3	14
α-helix	414-426	13
β-strand	435-441	7	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	500-501	2	16
β-strand	505	1	9
α-helix	518-534	17
α-helix	540-558	19
α-helix	570-581	12
α-helix	590-592	3
α-helix	594-596	3
α-helix	607-611	5
α-helix	617-623	7
β-strand	667	1	17

Chain C: 35 helices, 43 β-strands

Element	Residues	Length	Sheet
α-helix	45-54	10
β-strand	59-61	3	17
α-helix	65-68	4
β-strand	73-74	2	18
β-strand	77-78	2	18
β-strand	80	1	17
β-strand	91-93	3	17
α-helix	95-104	10
α-helix	113-116	4
α-helix	118-129	12
β-strand	131-137	7	19
α-helix	228-232	5
α-helix	234-237	4
β-strand	238	1	19
β-strand	242-247	6	19
α-helix	256-273	18
α-helix	278-286	9
β-strand	289-291	3	20
β-strand	294-295	2	20
α-helix	296-302	7
α-helix	308-317	10
β-strand	321-322	2	21
β-strand	325-327	3	22
β-strand	330-337	8	22
β-strand	342-347	6	23
β-strand	353-358	6	23
α-helix	359	1
β-strand	363-369	7	22
β-strand	372-379	8	22
β-strand	382-388	7	22
α-helix	393-407	15
α-helix	410-413	4
β-strand	423	1	24
α-helix	428	1
β-strand	429	1	24
α-helix	430-431	2
α-helix	432-442	11
α-helix	445-449	5
β-strand	453-455	3	25
β-strand	462	1	26
β-strand	465	1	27
β-strand	471	1	27
β-strand	474-476	3	25
β-strand	479-481	3	22
β-strand	482	1	26
α-helix	485-488	4
β-strand	494-495	2	21
β-strand	498-499	2	28
β-strand	505-506	2	28
β-strand	512-514	3	28
α-helix	516-518	3
β-strand	523	1	19
β-strand	530-532	3	20
α-helix	535-540	6
α-helix	545-556	12
α-helix	558-565	8
α-helix	571-574	4
α-helix	576-582	7
α-helix	587-605	19
α-helix	612-618	7
α-helix	620-622	3
α-helix	625-626	2
α-helix	634-636	3
β-strand	639-641	3	29
β-strand	649-651	3	29
β-strand	656	1	30
β-strand	659	1	30
β-strand	660-662	3	31
β-strand	667-669	3	31
β-strand	675-676	2	31
α-helix	683-685	3
α-helix	690-693	4
β-strand	698-700	3	32
α-helix	711-713	3
α-helix	714-719	6
α-helix	720-721	2
β-strand	725-729	5	32
β-strand	735-740	6	32

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	726	Influenza B virus (B/Memphis/13/2003)	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B	protein	752	Influenza B virus (B/Memphis/13/2003)	Q5V8Y6
Polymerase basic protein 2	C	protein	799	Influenza B virus (B/Memphis/13/2003)	Q5V8X3

Sequence of entity 1 (A), FASTA

>8RN2_1 Polymerase acidic protein (chains A)
MDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLDEEGKA
YTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKTKRFIE
VGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLSRLTELQAE
LSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGMRSYIDNIDPKGAIE
RNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMSDELGLANMTEGKSK
KPKTLAKECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNTISNEEMSNELQKTN
YAKWATGDGLTYQKIMKEVAIDDETMCQEEPKIPNKCRVAAWVQTEMNLLSTLTSKRALD
LPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLLNESNASMGKYKVIP
ITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDPRVDSGKWPKYTVFR
IGSLFVSGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEAIVEQESSIQGYDMT
KACFKGDRVNSPKTFSIGTQEGKLVKGSFGKALRVIFTKCLMHYVFGNAQLEGFSAESRR
LLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEWLGFEKEGSKVLESV
DEIMDE

Sequence of entity 2 (B), FASTA

>8RN2_2 RNA-directed RNA polymerase catalytic subunit (chains B)
MNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSNKGKQYISDV
TGCTMVDPTNGPLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAMETLMVTTVD
KLTQGRQTFDWTVCRNQPAATALNTTITSFRLNDLNGADKGGLIPFCQDIIDSLDRPEMT
FFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDAERGKLKRRA
IATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLSNCPPGGISM
TVTGDNTKWNECLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARLGKGFMITSK
TKRLKAQIPCPDLFSIPLERYNEETRAKLKKLKPFFNEEGTASLSPGMMMGMFNMLSTVL
GVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKLLGINMSKKK
SYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKNNMINNGMGP
ATAQTAIQLFIADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVADGGPNIYNL
RNLHIPEIVLKYNLMDPEYKGRLLHPQNPFVGHLSIEGIKEADITPAHGPVKKMDYDAVS
GTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQHSMLEAMAHR
LRMDARLDYESGRMSKDDFEKAMAHLGEIGYI

Sequence of entity 3 (C), FASTA

>8RN2_3 Polymerase basic protein 2 (chains C)
MTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKWAMCSNFPLA
LTKGDMANRIPLEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTEGFERVYESF
FLRKMRLDNATWGRITFGPVERVRKRVLLNPLTKEMPPDEASNVIMEILFPKEAGIPRES
TWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFIEMLHCLQGE
NWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVIDTEPLKSCL
AAIDGGDVACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNGTIQKIGIWD
GEEEFHVRCGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTRMFQGVRGEI
NFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNASDYTLKGVV
VTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMITYDTPKMWEM
GTTKELVQNTYQWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAGQYSGFARAV
LKQMRDQEVMKTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIEVRKGSPLFS
YNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDFKTIEELEKL
KPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSGWSHPQFEKG
GGSGGGSGGSAWSHPQFEK

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 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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