8RN6: Polymerase acidic protein

Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(E) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement). Determined by electron microscopy at 2.82 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.82 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 3
Atoms: 11,542
Mol. weight: 258.54 kDa
Released: 11 Sept 2024

Explore 8RN6 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RN6 contains 82 α-helices and 64 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: 39 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-23	13
α-helix	32-49	18
β-strand	53	1	1
β-strand	75	1	1
β-strand	77-79	3	2
α-helix	85-99	15
α-helix	101-104	4
β-strand	110-112	3	2
β-strand	117-124	8	2
α-helix	131-138	8
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	164-183	20
α-helix	207-214	8
α-helix	217	1
α-helix	223-230	8
α-helix	238-243	6
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	288	1	5
α-helix	290	1
β-strand	291-295	5	5
α-helix	302-312	11
α-helix	314-318	5
β-strand	323-326	4	5
α-helix	333-348	16
β-strand	355	1	5
α-helix	359-365	7
α-helix	372	1
β-strand	373-374	2	6
α-helix	377-382	6
β-strand	387-388	2	6
α-helix	389-391	3
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	450-467	18
β-strand	477-487	11	5
β-strand	492-502	11	5
β-strand	514-522	9	5
α-helix	526-528	3
α-helix	530-532	3
β-strand	537-545	9	5
β-strand	550-562	13	5
α-helix	564-572	9
α-helix	575-594	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: 36 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	27-28	2
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
α-helix	158-160	3
β-strand	162	1	11
α-helix	163-172	10
α-helix	173-175	3
β-strand	178-189	12	13
β-strand	202-213	12	13
α-helix	214-221	8
β-strand	223-225	3	14
β-strand	243-244	2	14
α-helix	246-263	18
β-strand	269	1	3
α-helix	276-291	16
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	354-359	6	6
β-strand	364-369	6	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	411-413	3
α-helix	414-425	12
β-strand	435-441	7	3
β-strand	445-452	8	3
α-helix	455-471	17
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	500-503	4	16
β-strand	505	1	9
α-helix	508-510	3
α-helix	518-535	18
α-helix	540-558	19
α-helix	572-581	10
α-helix	585-587	3
α-helix	590-592	3
α-helix	607-611	5
α-helix	612-614	3
α-helix	617-623	7
β-strand	667	1	17

Chain C: 7 helices, 8 β-strands

Element	Residues	Length	Sheet
α-helix	45-53	9
β-strand	59-60	2	17
α-helix	66-69	4
β-strand	73-74	2	18
β-strand	77-78	2	18
β-strand	80	1	17
β-strand	92-93	2	17
α-helix	95-104	10
α-helix	106-107	2
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-137	7	19
α-helix	228-232	5
β-strand	238	1	19
β-strand	242-247	6	19

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

>8RN6_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

>8RN6_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

>8RN6_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…
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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