8RN3: Polymerase acidic protein

Pseudo-symmetrical influenza B polymerase apo-dimer, encapsidase moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement). Determined by electron microscopy at 2.78 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.78 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 5
Atoms: 16,058
Mol. weight: 426.19 kDa
Ligands: MG
Released: 11 Sept 2024

Explore 8RN3 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RN3 contains 109 α-helices and 99 β-strands across 5 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: 37 helices, 25 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	77-79	3	1
α-helix	85-98	14
α-helix	102-104	3
β-strand	110-112	3	1
β-strand	117-124	8	1
α-helix	131-139	9
β-strand	144-149	6	1
β-strand	154-156	3	1
α-helix	164-183	20
α-helix	194-196	3
α-helix	207-213	7
α-helix	223-232	10
α-helix	238-244	7
β-strand	255-256	2	2
α-helix	259-261	3
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	3
α-helix	277-279	3
β-strand	288	1	4
β-strand	291-295	5	4
α-helix	302-312	11
α-helix	314-317	4
β-strand	324-326	3	4
α-helix	333-348	16
β-strand	355	1	4
α-helix	359-365	7
β-strand	373-374	2	5
α-helix	377-382	6
β-strand	387	1	5
α-helix	388-391	4
α-helix	393-396	4
β-strand	398	1	3
α-helix	401-410	10
β-strand	413	1	6
β-strand	416-417	2	4
α-helix	425-427	3
α-helix	430-446	17
β-strand	449	1	6
α-helix	450-467	18
β-strand	477-487	11	4
β-strand	492-502	11	4
β-strand	514-522	9	4
α-helix	530-532	3
β-strand	537-545	9	4
β-strand	550-562	13	4
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	615-619	5	7
β-strand	624-627	4	7
α-helix	629-645	17
α-helix	649-670	22
β-strand	675-676	2	2
α-helix	679-687	9
α-helix	694-715	22

Chain B: 36 helices, 32 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	7
α-helix	5-7	3
α-helix	8-11	4
α-helix	14-17	4
β-strand	22	1	8
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	119-121	3
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-152	14
α-helix	158-160	3
β-strand	162	1	10
α-helix	163-172	10
α-helix	173-175	3
β-strand	178-186	9	12
β-strand	189	1	13
β-strand	202	1	13
β-strand	205-213	9	12
α-helix	214-221	8
β-strand	223-226	4	14
α-helix	227	1
β-strand	242-244	3	14
β-strand	245	1	11
α-helix	246-263	18
β-strand	269	1	2
α-helix	276-291	16
α-helix	294	1
β-strand	298-305	8	2
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	5
β-strand	364-368	5	5
α-helix	369	1
α-helix	370-375	6
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	2
β-strand	445-452	8	2
α-helix	455-472	18
β-strand	476	1	15
β-strand	482-485	4	2
β-strand	488-491	4	16
β-strand	494-497	4	16
β-strand	500-503	4	16
β-strand	505	1	8
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	607-611	5
α-helix	612-614	3
α-helix	617-623	7
β-strand	667	1	17

Chain C: 32 helices, 38 β-strands

Element	Residues	Length	Sheet
α-helix	45-53	9
β-strand	59-61	3	17
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	228-231	4
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	296-303	8
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
β-strand	363-369	7	22
β-strand	372-379	8	22
β-strand	382-389	8	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	22
β-strand	474-476	3	25
β-strand	479-482	4	22
α-helix	485-488	4
β-strand	494-495	2	21
β-strand	498-499	2	26
β-strand	505-506	2	26
β-strand	512-514	3	26
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	587-602	16
α-helix	603-607	5
α-helix	612-618	7
α-helix	620-622	3
α-helix	625-626	2
β-strand	639-641	3	27
β-strand	649-651	3	27
β-strand	660-662	3	28
β-strand	667-669	3	28
β-strand	675-676	2	28
α-helix	684-687	4
α-helix	690-692	3
β-strand	698-700	3	29
α-helix	714-719	6
α-helix	721	1
β-strand	725-729	5	29
β-strand	735-740	6	29

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	361-365	5
α-helix	372	1
β-strand	373-374	2	30
α-helix	377-382	6
β-strand	387-388	2	30

Chain E: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	354-359	6	30
β-strand	364-369	6	30
α-helix	378-380	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A, D	protein	726	Influenza B virus (B/Memphis/13/2003)	Q5V8Z9
RNA-directed RNA polymerase catalytic subunit	B, E	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, D), FASTA

>8RN3_1 Polymerase acidic protein (chains A, D)
MDTFITRNFQTTIIQKAKNTMAEFSEDPELQPAMLFNICVHLEVCYVISDMNFLDEEGKA
YTALEGQGKEQNLRPQYEVIEGMPRTIAWMVQRSLAQEHGIETPKYLADLFDYKTKRFIE
VGITKGLADDYFWKKKEKLGNSMELMIFSYNQDYSLSNESSLDEEGKGRVLSRLTELQAE
LSLKNLWQVLIGEEDVEKGIDFKLGQTISRLRDISVPAGFSNFEGMRSYIDNIDPKGAIE
RNLARMSPLVSVTPKKLTWEDLRPIGPHIYNHELPEVPYNAFLLMSDELGLANMTEGKSK
KPKTLAKECLEKYSTLRDQTDPILIMKSEKANENFLWKLWRDCVNTISNEEMSNELQKTN
YAKWATGDGLTYQKIMKEVAIDDETMCQEEPKIPNKCRVAAWVQTEMNLLSTLTSKRALD
LPEIGPDVAPVEHVGSERRKYFVNEINYCKASTVMMKYVLFHTSLLNESNASMGKYKVIP
ITNRVVNEKGESFDMLYGLAVKGQSHLRGDTDVVTVVTFEFSSTDPRVDSGKWPKYTVFR
IGSLFVSGREKSVYLYCRVNGTNKIQMKWGMEARRCLLQSMQQMEAIVEQESSIQGYDMT
KACFKGDRVNSPKTFSIGTQEGKLVKGSFGKALRVIFTKCLMHYVFGNAQLEGFSAESRR
LLLLIQALKDRKGPWVFDLEGMYSGIEECISNNPWVIQSAYWFNEWLGFEKEGSKVLESV
DEIMDE

Sequence of entity 2 (B, E), FASTA

>8RN3_2 RNA-directed RNA polymerase catalytic subunit (chains B, E)
MNINPYFLFIDVPIQAAISTTFPYTGVPPYSHGTGTGYTIDTVIRTHEYSNKGKQYISDV
TGCTMVDPTNGPLPEDNEPSAYAQLDCVLEALDRMDEEHPGLFQAASQNAMETLMVTTVD
KLTQGRQTFDWTVCRNQPAATALNTTITSFRLNDLNGADKGGLIPFCQDIIDSLDRPEMT
FFSVKNIKKKLPAKNRKGFLIKRIPMKVKDKITKVEYIKRALSLNTMTKDAERGKLKRRA
IATAGIQIRGFVLVVENLAKNICENLEQSGLPVGGNEKKAKLSNAVAKMLSNCPPGGISM
TVTGDNTKWNECLNPRIFLAMTERITRDSPIWFRDFCSIAPVLFSNKIARLGKGFMITSK
TKRLKAQIPCPDLFSIPLERYNEETRAKLKKLKPFFNEEGTASLSPGMMMGMFNMLSTVL
GVAALGIKNIGNKEYLWDGLQSSDDFALFVNAKDEETCMEGINDFYRTCKLLGINMSKKK
SYCNETGMFEFTSMFYRDGFVSNFAMELPSFGVAGVNESADMAIGMTIIKNNMINNGMGP
ATAQTAIQLFIADYRYTYKCHRGDSKVEGKRMKIIKELWENTKGRDGLLVADGGPNIYNL
RNLHIPEIVLKYNLMDPEYKGRLLHPQNPFVGHLSIEGIKEADITPAHGPVKKMDYDAVS
GTHSWRTKRNRSILNTDQRNMILEEQCYAKCCNLFEACFNSASYRKPVGQHSMLEAMAHR
LRMDARLDYESGRMSKDDFEKAMAHLGEIGYI

Sequence of entity 3 (C), FASTA

>8RN3_3 Polymerase basic protein 2 (chains C)
MTLAKIELLKQLLRDNEAKTVLKQTTVDQYNIIRKFNTSRIEKNPSLRMKWAMCSNFPLA
LTKGDMANRIPLEYKGIQLKTNAEDIGTKGQMCSIAAVTWWNTYGPIGDTEGFERVYESF
FLRKMRLDNATWGRITFGPVERVRKRVLLNPLTKEMPPDEASNVIMEILFPKEAGIPRES
TWIHRELIKEKREKLKGTMITPIVLAYMLERELVARRRFLPVAGATSAEFIEMLHCLQGE
NWRQIYHPGGNKLTESRSQSMIVACRKIIRRSIVASNPLELAVEIANKTVIDTEPLKSCL
AAIDGGDVACDIIRAALGLKIRQRQRFGRLELKRISGRGFKNDEEILIGNGTIQKIGIWD
GEEEFHVRCGECRGILKKSKMKLEKLLINSAKKEDMRDLIILCMVFSQDTRMFQGVRGEI
NFLNRAGQLLSPMYQLQRYFLNRSNDLFDQWGYEESPKASELHGINESMNASDYTLKGVV
VTRNVIDDFSSTETEKVSITKNLSLIKRTGEVIMGANDVSELESQAQLMITYDTPKMWEM
GTTKELVQNTYQWVLKNLVTLKAQFLLGKEDMFQWDAFEAFESIIPQKMAGQYSGFARAV
LKQMRDQEVMKTDQFIKLLPFCFSPPKLRSNGEPYQFLKLVLKGGGENFIEVRKGSPLFS
YNPQTEVLTICGRMMSLKGKIEDEERNRSMGNAVLAGFLVSGKYDPDLGDFKTIEELEKL
KPGEKANILLYQGKPVKVVKRKRYSALSNDISQGIKRQRMTVESMGWALSGWSHPQFEKG
GGSGGGSGGSAWSHPQFEK

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	3

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…
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

Browse structure collections

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