8RN4: Polymerase acidic protein

Pseudo-symmetrical influenza B polymerase apo-dimer, ENDO(T) moiety (from "Influenza B polymerase pseudo-symmetrical dimer" | Local refinement). Determined by electron microscopy at 2.87 Å resolution. Released 11 Sept 2024.

Method: Electron microscopy
Resolution: 2.87 Å
Organism: Influenza B virus (B/Memphis/13/2003)
Chains: 5
Atoms: 13,718
Mol. weight: 426.16 kDa
Ligands: MG
Released: 11 Sept 2024

Explore 8RN4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8RN4 contains 92 α-helices and 75 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: 36 helices, 30 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-23	13
α-helix	32-49	18
β-strand	53-54	2	1
β-strand	60-61	2	1
β-strand	74-75	2	1
β-strand	77-79	3	2
α-helix	85-99	15
α-helix	102-104	3
α-helix	107-108	2
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	153-156	4	2
α-helix	164-183	20
α-helix	207-213	7
α-helix	217	1
α-helix	223-232	10
α-helix	238-245	8
β-strand	255-256	2	3
α-helix	267-270	4
α-helix	275	1
β-strand	276	1	4
α-helix	277-278	2
β-strand	288	1	5
β-strand	291-295	5	5
α-helix	302-312	11
α-helix	314-318	5
β-strand	324-326	3	5
α-helix	333-348	16
β-strand	355	1	5
α-helix	361-365	5
α-helix	372	1
β-strand	373-374	2	6
α-helix	377-382	6
β-strand	387	1	6
α-helix	388-391	4
α-helix	393-396	4
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	430-447	18
β-strand	449	1	7
α-helix	450-471	22
β-strand	476-487	12	5
β-strand	492-503	12	5
β-strand	515-522	8	5
α-helix	530-532	3
β-strand	537-545	9	5
β-strand	550-560	11	5
α-helix	564-571	8
α-helix	575-594	20
α-helix	600-604	5
β-strand	607	1	8
β-strand	610	1	8
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	3
α-helix	679-687	9
α-helix	694-715	22

Chain B: 38 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-7	3
α-helix	8-11	4
α-helix	18-21	4
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	119-123	5
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	163-173	11
β-strand	178-188	11	13
β-strand	203-213	11	13
α-helix	214-222	9
β-strand	223-228	6	14
β-strand	240-244	5	14
β-strand	245	1	12
α-helix	246-263	18
β-strand	269	1	3
α-helix	277-292	16
α-helix	294	1
β-strand	298-303	6	3
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	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	1	14
β-strand	401-403	3	14
α-helix	414-425	12
β-strand	435-442	8	3
β-strand	445-452	8	3
α-helix	455-471	17
β-strand	482-485	4	3
β-strand	488-491	4	15
β-strand	494-497	4	15
β-strand	500-502	3	15
α-helix	518-536	19
α-helix	540-558	19
α-helix	570-581	12
α-helix	585-587	3
α-helix	590-592	3
α-helix	607-610	4
α-helix	617-623	7
β-strand	641-642	2	16
β-strand	654-655	2	16
α-helix	665-666	2
β-strand	667	1	17
α-helix	668	1
α-helix	680-698	19
α-helix	700-702	3
β-strand	712	1	18
α-helix	713-731	19
α-helix	736-749	14

Chain C: 15 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	2-13	12
α-helix	16-24	9
β-strand	26	1	18
α-helix	30-33	4
α-helix	45-53	9
β-strand	59-60	2	17
α-helix	61-63	3
α-helix	65-69	5
β-strand	74	1	19
β-strand	77	1	19
β-strand	80-81	2	17
β-strand	92-93	2	17
α-helix	95-103	9
α-helix	113-116	4
α-helix	118-128	11
β-strand	131-136	6	20
β-strand	143-148	6	21
β-strand	156	1	22
α-helix	158-169	12
α-helix	171-173	3
α-helix	185-194	10
α-helix	202-213	12
β-strand	214	1	22
β-strand	217-222	6	21
α-helix	228-231	4
α-helix	234-236	3
β-strand	243-247	5	20

Chain D: 3 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	361-365	5
β-strand	373-374	2	23
α-helix	377-382	6
β-strand	387	1	23
α-helix	388-390	3

Chain E: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	355-359	5	23
β-strand	364-368	5	23

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

>8RN4_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

>8RN4_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

>8RN4_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	2

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…
6QCW 2.88 Å, Crystal structure of influenza B polymerase initiation state with capped 14-mer RNA primer

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