5M3H: Bat influenza A/H17N10 polymerase

Bat influenza A/H17N10 polymerase bound to four heptad repeats of serine 5 phosphorylated Pol II CTD. Determined by X-ray diffraction at 2.5 Å resolution. Released 21 Dec 2016.

Method: X-ray diffraction
Resolution: 2.5 Å
Organisms: Influenza A virus, Homo sapiens
Chains: 7
Atoms: 18,529
Mol. weight: 281.1 kDa
Ligands: ZN, PO4
Released: 21 Dec 2016

Explore 5M3H in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5M3H contains 115 α-helices and 103 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: 32 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	4-8	5
α-helix	11-18	8
α-helix	37-49	13
β-strand	53-54	2	1
β-strand	60-61	2	1
β-strand	73-74	2	1
β-strand	76	1	2
α-helix	84-97	14
β-strand	109-111	3	2
β-strand	116-120	5	2
α-helix	128-134	7
β-strand	144-147	4	2
β-strand	155-156	2	2
α-helix	157-159	3
α-helix	165-178	14
α-helix	181-184	4
α-helix	209-217	9
α-helix	226-235	10
α-helix	241-248	8
β-strand	258-259	2	3
α-helix	265-271	7
β-strand	275	1	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	5
α-helix	359-364	6
α-helix	371	1
β-strand	372-374	3	6
α-helix	376-379	4
β-strand	386-387	2	6
α-helix	391-395	5
β-strand	397	1	4
α-helix	400-409	10
β-strand	412	1	7
β-strand	415-416	2	5
α-helix	424-426	3
α-helix	429-446	18
β-strand	448	1	7
α-helix	449-470	22
β-strand	475-486	12	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	576-578	3
α-helix	579-598	20
α-helix	603-608	6
β-strand	614-619	6	8
β-strand	622-626	5	8
α-helix	628-644	17
α-helix	648-668	21
β-strand	674-675	2	3
α-helix	678-686	9
α-helix	693-713	21

Chain B: 43 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	8
α-helix	5-10	6
α-helix	15-21	7
α-helix	27-29	3
α-helix	36-49	14
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	119-122	4
β-strand	128-130	3	11
β-strand	135-137	3	11
α-helix	139-152	14
α-helix	157-160	4
β-strand	162	1	10
α-helix	163-172	10
α-helix	173-175	3
β-strand	179-193	15	12
β-strand	198-212	15	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	246-263	18
β-strand	269	1	3
α-helix	275-291	17
β-strand	298-305	8	3
β-strand	306	1	15
α-helix	315-325	11
α-helix	331-337	7
α-helix	339-345	7
β-strand	348-349	2	13
β-strand	355-359	5	6
β-strand	364-368	5	6
α-helix	372-375	4
α-helix	383-395	13
β-strand	396-397	2	13
β-strand	400-402	3	13
α-helix	415-425	11
α-helix	429-432	4
β-strand	436-443	8	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	541-558	18
α-helix	573-582	10
α-helix	586-588	3
α-helix	591-593	3
α-helix	595-597	3
α-helix	601-603	3
α-helix	608-612	5
α-helix	613-615	3
α-helix	618-624	7
β-strand	632	1	17
α-helix	637-639	3
β-strand	642-645	4	18
β-strand	653-656	4	18
β-strand	666	1	17
β-strand	667-668	2	19
α-helix	669-671	3
α-helix	673-676	4
α-helix	678-681	4
α-helix	682-699	18
α-helix	701-704	4
β-strand	713	1	20
α-helix	714-731	18
α-helix	737-752	16

Chain C: 40 helices, 42 β-strands

Element	Residues	Length	Sheet
α-helix	1-12	12
α-helix	14-22	9
β-strand	24	1	20
α-helix	25-32	8
α-helix	37-40	4
α-helix	43-50	8
β-strand	57-59	3	19
α-helix	63-66	4
β-strand	70	1	21
β-strand	76	1	21
β-strand	78-82	5	19
α-helix	83	1
β-strand	89-91	3	19
α-helix	93-102	10
α-helix	111-114	4
α-helix	116-126	11
β-strand	129-135	7	22
β-strand	141-146	6	23
β-strand	154	1	24
α-helix	156-167	12
α-helix	169-171	3
α-helix	180-192	13
α-helix	200-211	12
β-strand	212	1	24
β-strand	215-220	6	23
α-helix	226-229	4
α-helix	232-235	4
β-strand	236	1	22
β-strand	240-245	6	22
α-helix	252-271	20
α-helix	276-286	11
β-strand	288-289	2	25
β-strand	292-293	2	25
α-helix	294-300	7
α-helix	306-314	9
α-helix	317-319	3
β-strand	322-325	4	26
β-strand	328-335	8	26
β-strand	338-345	8	27
β-strand	351-358	8	27
β-strand	361-366	6	26
β-strand	370-377	8	26
β-strand	380-388	9	26
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	28
β-strand	461	1	26
β-strand	462-463	2	29
β-strand	469-470	2	29
β-strand	473-475	3	28
β-strand	478-480	3	26
β-strand	496-498	3	30
β-strand	504-506	3	30
β-strand	511-513	3	30
α-helix	515-517	3
β-strand	529-530	2	25
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	586-605	20
α-helix	612-618	7
α-helix	619-622	4
α-helix	625-627	3
β-strand	635-640	6	31
β-strand	643-648	6	31
β-strand	657-659	3	32
β-strand	664-667	4	32
β-strand	670-671	2	32
α-helix	674-676	3
α-helix	677-679	3
β-strand	687	1	33
β-strand	694-699	6	33
α-helix	702-704	3
β-strand	707-708	2	33
α-helix	710-715	6
β-strand	721-727	7	33
β-strand	730-736	7	33

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Polymerase acidic protein	A	protein	728	Influenza A virus	H6QM92
RNA-directed RNA polymerase catalytic subunit	B	protein	776	Influenza A virus	H6QM91
Polymerase basic protein 2	C	protein	797	Influenza A virus	H6QM90
RNA (5'-r(upapupapcpcpupcpupgpcpup*u)-3')	R	RNA	18	Influenza A virus
RNA 5'-paguaguaacaagaggg	V	RNA	16	Influenza A virus
Tyr-ser-pro-thr-sep-pro	X, Y	protein	28	Homo sapiens	P24928 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5M3H_1 Polymerase acidic protein (chains A)
GSGSMENFVRTNFNPMILERAEKTMKEYGENPQNEGNKFAAISTHMEVCFMYSDFHFIDL
EGNTIVKENDDDNAMLKHRFEIIEGQERNIAWTIVNSICNMTENSKPRFLPDLYDYKTNK
FIEIGVTRRKVEDYYYEKASKLKGENVYIHIFSFDGEEMATDDEYILDEESRARIKTRLF
VLRQELATAGLWDSFRQSEKGEETLEEEFSYPPTFQRLANQSLPPSFKDYHQFKAYVSSF
KANGNIEAKLGAMSEKVNAQIESFDPRTIRELELPEGKFCTQRSKFLLMDAMKLSVLNPA
HEGEGIPMKDAKACLDTFWGWKKATIIKKHEKGVNTNYLMIWEQLLESIKEMEGKFLNLK
KTNHLKWGLGEGQAPEKMDFEDCKEVPDLFQYKSEPPEKRKLASWIQSEFNKASELTNSN
WIEFDELGNDVAPIEHIASRRRNFFTAEVSQCRASEYIMKAVYINTALLNSSCTAMEEYQ
VIPIITKCRDTSGQRRTNLYGFIIKGRSHLRNDTDVVNFISLEFSLTDPRNEIHKWEKYC
VLEIGDMEIRTSISTIMKPVYLYVRTNGTSKIKMKWGMEMRRCLLQSLQQVESMIEAESA
VKEKDMTEPFFRNRENDWPIGESPQGIEKGTIGKVCRVLLAKSVFNSIYASAQLEGFSAE
SRKLLLLIQAFRDNLDPGTFDLKGLYEAIEECIINDPWVLLNASWFNSFLKAVQLSMGSG
SGENLYFQ

Sequence of entity 2 (B), FASTA

>5M3H_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

>5M3H_3 Polymerase basic protein 2 (chains C)
GSGSGSGSGMERIKELMEMVKNSRMREILTTTSVDHMAVIKKYTSGRQEKNPALRMKWMM
AMKYPISASSRIREMIPEKDEDGNTLWTNTKDAGSNRVLVSPNAVTWWNRAGPVSDVVHY
PRVYKMYFDRLERLTHGTFGPVKFYNQVKVRKRVDINPGHKDLTSREAQEVIMEVVFPNE
VGARTLSSDAQLTITKEKKEELKNCKISPIMVAYMLERELVRRTRFLPIAGATSSTYVEV
LHLTQGTCWEQQYTPGGEAENDDLDQTLIIASRNIVRRSIVAIDPLASLLSMCHTTSISS
EPLVEILRSNPTDEQAVNICKAALGIRINNSFSFGGYNFKRVKGSSQRTEKAVLTGNLQT
LTMTIFEGYEEFNVSGKRASAVLKKGAQRLIQAIIGGRTLEDILNLMITLMVFSQEEKML
KAVRGDLNFVNRANQRLNPMYQLLRHFQKDSSTLLKNWGTEEIDPIMGIAGIMPDGTINK
TQTLMGVRLSQGGVDEYSFNERIRVNIDKYLRVRNEKGELLISPEEVSEAQGQEKLPINY
NSSLMWEVNGPESILTNTYHWIIKNWELLKTQWMTDPTVLYNRIEFEPFQTLIPKGNRAI
YSGFTRTLFQQMRDVEGTFDSIQIIKLLPFSAHPPSLGRTQFSSFTLNIRGAPLRLLIRG
NSQVFNYNQMENVIIVLGKSVGSPERSILTESSSIESAVLRGFLILGKANSKYGPVLTIG
ELDKLGRGEKANVLIGQGDTVLVMKRKRDSSILTDSQTALKRIRLEESKGWSHPQFEKGW
SHPQFEKGSGSENLYFQ

Sequence of entity 4 (R), FASTA

>5M3H_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

>5M3H_5 RNA 5'-pAGUAGUAACAAGAGGG (chains V)
AGUAGUAACAAGAGGG

Sequence of entity 6 (X, Y), FASTA

>5M3H_6 TYR-SER-PRO-THR-SEP-PRO (chains X, Y)
YSPTSPSYSPTSPSYSPTSPSYSPTSPS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
PO4	Phosphate ion	O4 P	15

Primary citation

Structural basis of an essential interaction between influenza polymerase and Pol II CTD. Lukarska, M., Fournier, G., Pflug, A. et al. Nature (2017) 541:117-121. DOI 10.1038/nature20594 · 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…
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…
6EVK 2.9 Å, Crystal structure of bat influenza A/H17N10 polymerase with viral RNA promoter and cap…

Browse structure collections

About this viewer

MolViewer shows 5M3H directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.