6EVK: Polymerase acidic protein

Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap analogue m7GTP. Determined by X-ray diffraction at 2.9 Å resolution. Released 13 Dec 2017.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10)), Influenza A virus
Chains: 5
Atoms: 18,166
Mol. weight: 277.03 kDa
Ligands: MGP, PO4, ZN
Released: 13 Dec 2017

Explore 6EVK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6EVK contains 110 α-helices and 98 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: 34 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	2-8	7
α-helix	11-21	11
α-helix	32-49	18
β-strand	52-54	3	1
β-strand	60-62	3	1
β-strand	73-74	2	1
β-strand	76-78	3	2
α-helix	84-97	14
α-helix	100-103	4
β-strand	109-111	3	2
β-strand	116-123	8	2
α-helix	128-138	11
β-strand	144-149	6	2
β-strand	154-156	3	2
α-helix	157-159	3
α-helix	165-184	20
α-helix	209-217	9
α-helix	226-234	9
α-helix	241-248	8
β-strand	258-259	2	3
α-helix	260	1
α-helix	265-268	4
β-strand	274-275	2	4
α-helix	276-278	3
β-strand	290-293	4	5
α-helix	303-311	9
β-strand	317-324	8	5
α-helix	331-346	16
β-strand	354-355	2	6
α-helix	359-364	6
α-helix	371	1
β-strand	372-374	3	7
α-helix	377-379	3
β-strand	385-387	3	7
α-helix	388-389	2
α-helix	391-395	5
β-strand	396-397	2	4
α-helix	401-409	9
β-strand	412	1	8
β-strand	415-416	2	5
α-helix	420-422	3
α-helix	424-426	3
α-helix	429-446	18
β-strand	448	1	8
α-helix	449-470	22
β-strand	475-476	2	6
β-strand	477-486	10	5
β-strand	491-501	11	5
β-strand	512-521	10	5
α-helix	525-532	8
β-strand	536-546	11	5
β-strand	551-566	16	5
α-helix	567-574	8
α-helix	578-598	21
α-helix	603-608	6
β-strand	614-618	5	9
β-strand	623-626	4	9
α-helix	628-644	17
α-helix	648-668	21
β-strand	674-675	2	3
α-helix	678-687	10
α-helix	693-713	21

Chain B: 40 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	9
α-helix	5-7	3
α-helix	8-11	4
α-helix	14-21	8
α-helix	27-29	3
α-helix	36-50	15
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
α-helix	120-122	3
β-strand	127-130	4	11
β-strand	135-138	4	11
α-helix	139-152	14
α-helix	158-160	3
α-helix	163-172	10
β-strand	178-191	14	12
β-strand	200-213	14	12
α-helix	214-221	8
β-strand	223-224	2	13
β-strand	225-228	4	14
α-helix	229-230	2
β-strand	240-243	4	14
β-strand	245	1	11
α-helix	249-263	15
β-strand	269	1	3
α-helix	275-291	17
β-strand	298-305	8	3
β-strand	306	1	15
α-helix	315-326	12
α-helix	331-345	15
β-strand	348-350	3	13
β-strand	355-359	5	7
β-strand	364-368	5	7
α-helix	370-373	4
α-helix	383-393	11
β-strand	396-397	2	13
β-strand	400-402	3	13
α-helix	415-425	11
α-helix	429-432	4
β-strand	437-443	7	3
β-strand	446-453	8	3
α-helix	456-471	16
β-strand	477	1	15
β-strand	483-486	4	3
β-strand	489-492	4	16
β-strand	495-498	4	16
β-strand	501	1	16
α-helix	506-511	6
α-helix	519-536	18
α-helix	541-559	19
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	601-603	3
α-helix	608-612	5
α-helix	613-615	3
α-helix	618-624	7
α-helix	637-639	3
β-strand	642-645	4	17
β-strand	653-656	4	17
β-strand	667-668	2	18
α-helix	669-671	3
α-helix	673-676	4
α-helix	681-699	19
α-helix	701-704	4
β-strand	713	1	19
α-helix	714-731	18
α-helix	737-752	16

Chain C: 36 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	2-12	11
α-helix	14-22	9
β-strand	24	1	19
α-helix	25-32	8
α-helix	37-40	4
α-helix	43-51	9
β-strand	57-60	4	18
α-helix	63-66	4
β-strand	70	1	20
β-strand	76	1	20
β-strand	78-82	5	18
α-helix	83	1
β-strand	88-91	4	18
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	21
β-strand	141-146	6	22
α-helix	156-167	12
α-helix	180-192	13
α-helix	200-211	12
β-strand	215-220	6	22
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	21
β-strand	240-245	6	21
α-helix	252-272	21
α-helix	276-286	11
β-strand	288-289	2	23
β-strand	293	1	23
α-helix	294-299	6
α-helix	306-315	10
β-strand	323-325	3	24
β-strand	328-335	8	24
β-strand	338-345	8	25
β-strand	351-358	8	25
β-strand	361-366	6	24
β-strand	370-377	8	24
β-strand	380-388	9	24
α-helix	391-404	14
α-helix	408-412	5
α-helix	426-429	4
α-helix	430-440	11
α-helix	443-449	7
β-strand	451-453	3	26
β-strand	460-461	2	24
β-strand	462-463	2	27
β-strand	469-470	2	27
β-strand	473-475	3	26
β-strand	478-481	4	24
β-strand	496-498	3	28
β-strand	504-506	3	28
β-strand	511-513	3	28
α-helix	518-521	4
β-strand	529-530	2	23
α-helix	542-555	14
α-helix	557-565	9
α-helix	568-572	5
α-helix	575-577	3
α-helix	578-582	5
α-helix	588-605	18
α-helix	612-618	7
α-helix	619-622	4
β-strand	635-639	5	29
β-strand	644-648	5	29
β-strand	656-659	4	30
β-strand	664-667	4	30
β-strand	670-673	4	30
α-helix	674-676	3
α-helix	677-679	3
β-strand	687-691	5	31
β-strand	694-699	6	31
α-helix	702-704	3
β-strand	708	1	31
β-strand	721-727	7	31
β-strand	730-736	7	31

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	738	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM92
RNA-directed RNA polymerase catalytic subunit	B	protein	776	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM91
Polymerase basic protein 2	C	protein	809	Influenza A virus (A/little yellow-shouldered bat/Guatemala/060/2010(H17N10))	H6QM90
RNA (5'-r(upapupapcpcpupcpupgpcpup*u)-3')	R	RNA	18	Influenza A virus
RNA (5'-r(papgpupapgpupapapcpapapgpapgpgpg)-3')	V	RNA	16	Influenza A virus

Sequence of entity 1 (A), FASTA

>6EVK_1 Polymerase acidic protein (chains A)
GSHHHHHHHHGSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCF
MYSDFHFIDLEGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFL
PDLYDYKTNKFIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEE
SRARIKTRLFVLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDY
HQFKAYVSSFKANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMD
AMKLSVLNPAHEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIK
EMEGKFLNLKKTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEF
NKASELTNSNWIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLN
SSCTAMEEYQVIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPR
NEIHKWEKYCVLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQ
VESMIEAESAVKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYA
SAQLEGFSAESRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFL
KAVQLSMGSGSGENLYFQ

Sequence of entity 2 (B), FASTA

>6EVK_2 RNA-directed RNA polymerase catalytic subunit (chains B)
GSGSGSGSGMDVNPMLIFLKVPVQNAISTTFPYTGDPPYSHGTGTGYTMDTVIRTHDYSS
RGIWKTNSETGAQQLNPIDGPLPEDNEPSGYAQTDCVLELIEGLDRSHPGLFETACQETI
DAIQQTRVDKLTQGRQTYDWTLNRNQPAATALANTIEVFRKNGYKLNESGRLIDFLKDVL
LSFENDSMEVTTHFQKKKRIRDNHSKKMITQRTIGKKRVKLTKKNYLIRALTLNTMTKDA
ERGKLKRRAIATPGMQIRGFVYFVELLARNICERLEQSGLPVGGNEKKAKLANVIKKMMA
KSTDEELSYTITGDNTKWNENQNPRIFLAMVLRITAGQPEWFRDLLAVAPIMFSNKVARL
GRGYMFESKSMHLRTQISAENLSDINLRYFNEDTKKKIEKIRHLMVEGTASLSPGMMMGM
FNMLSTVLGVSVLNLGQREILKRTYWWDGLQSSDDFALIINGHFKEDIQQGVNHFYRTCK
LVGINMSQKKSYINKTGTFEFTSFFYRYGFVANFSMELPSFGVAGNNESADMSIGTTVIK
TNMINNDLGPATAQMAIQLFIKDYRYTYRCHRGDTNLETRRTKSIKRLWTETISKAGLLV
ADGGPNPYNLRNLHIPEVCLKWSLMDPDYRGRLCNPNNPFVHHMEVESTNLAVVMPAHGP
AKSLEYDAVATTHSWTPKRNRSILNTNQRGILEDERIYQKCCQVFEKFFPSSTYRRPIGM
ASMLDAMLSRARIDARIDLESGRISSQDFSEITNTCKAIEALKRQGSGSGENLYFQ

Sequence of entity 3 (C), FASTA

>6EVK_3 Polymerase basic protein 2 (chains C)
GSGSGSGSGMERIKELMEMVKNSRMREILTTTSVDHMAVIKKYTSGRQEKNPALRMKWMM
AMKYPISASSRIREMIPEKDEDGNTLWTNTKDAGSNRVLVSPNAVTWWNRAGPVSDVVHY
PRVYKMYFDRLERLTHGTFGPVKFYNQVKVRKRVDINPGHKDLTSREAQEVIMEVVFPNE
VGARTLSSDAQLTITKEKKEELKNCKISPIMVAYMLERELVRRTRFLPIAGATSSTYVEV
LHLTQGTCWEQQYTPGGEAENDDLDQTLIIASRNIVRRSIVAIDPLASLLSMCHTTSISS
EPLVEILRSNPTDEQAVNICKAALGIRINNSFSFGGYNFKRVKGSSQRTEKAVLTGNLQT
LTMTIFEGYEEFNVSGKRASAVLKKGAQRLIQAIIGGRTLEDILNLMITLMVFSQEEKML
KAVRGDLNFVNRANQRLNPMYQLLRHFQKDSSTLLKNWGTEEIDPIMGIAGIMPDGTINK
TQTLMGVRLSQGGVDEYSFNERIRVNIDKYLRVRNEKGELLISPEEVSEAQGQEKLPINY
NSSLMWEVNGPESILTNTYHWIIKNWELLKTQWMTDPTVLYNRIEFEPFQTLIPKGNRAI
YSGFTRTLFQQMRDVEGTFDSIQIIKLLPFSAHPPSLGRTQFSSFTLNIRGAPLRLLIRG
NSQVFNYNQMENVIIVLGKSVGSPERSILTESSSIESAVLRGFLILGKANSKYGPVLTIG
ELDKLGRGEKANVLIGQGDTVLVMKRKRDSSILTDSQTALKRIRLEESKGWSHPQFEKGG
GSGGGSGGSAWSHPQFEKGRSGGENLYFQ

Sequence of entity 4 (R), FASTA

>6EVK_4 RNA (5'-R(*UP*AP*UP*AP*CP*CP*UP*CP*UP*GP*CP*UP*U)-3') (chains R)
UAUACCUCUGCUUCUGCU

Sequence of entity 5 (V), FASTA

>6EVK_5 RNA (5'-R(P*AP*GP*UP*AP*GP*UP*AP*AP*CP*AP*AP*GP*AP*GP*GP*G)-3') (chains V)
AGUAGUAACAAGAGGG

Ligands and cofactors

ID	Name	Formula	Copies
MGP	7-methyl-guanosine-5'-triphosphate	C11 H19 N5 O14 P3	1
PO4	Phosphate ion	O4 P	12
ZN	Zinc ion	Zn	1

Primary citation

Capped RNA primer binding to influenza polymerase and implications for the mechanism of cap-binding inhibitors. Pflug, A., Gaudon, S., Resa-Infante, P. et al. Nucleic Acids Res (2018) 46:956-971. DOI 10.1093/nar/gkx1210 · PubMed

Other PDB entries of the same protein (UniProt H6QM92), best resolution first:

9F37 1.91 Å, Replication-like initiation state of influenza polymerase with GTP and CTP at…
9F2R 1.96 Å, Influenza A/H17N10 polymerase with bound promoter and 3' end of template in active site
6SZU 2.41 Å, Bat Influenza A polymerase pre-termination complex with pyrophosphate using 44-mer vRNA…
5M3H 2.5 Å, Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5…
6SZV 2.5 Å, Bat Influenza A polymerase elongation complex with incoming UTP analogue (core +…
6T0N 2.54 Å, Bat Influenza A polymerase pre-initiation complex
4WSB 2.65 Å, Bat Influenza A polymerase with bound vRNA promoter
4NFZ 2.7 Å, Crystal structure of polymerase subunit PA N-terminal endonuclease domain from…
6FHH 2.7 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to…
6TW1 2.7 Å, Bat Influenza A polymerase termination complex with pyrophosphate using 44-mer vRNA…
6FHI 2.8 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter bound to…
6T0R 2.82 Å, Bat Influenza A polymerase product dissociation complex using 44-mer vRNA template with…

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