6QSN: Yellow fever virus polymerase NS5A

Crystal structure of Yellow fever virus polymerase NS5A. Determined by X-ray diffraction at 3.0 Å resolution. Released 16 Oct 2019.

Method: X-ray diffraction
Resolution: 3.0 Å
Organism: Yellow fever virus 17D
Chains: 2
Atoms: 14,318
Mol. weight: 209.9 kDa
Ligands: ZN, SAH
Released: 16 Oct 2019

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

Secondary structure: helices and β-sheets

6QSN contains 116 α-helices and 78 β-strands across 2 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: 59 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-28	8
β-strand	33-34	2	1
α-helix	38-45	8
β-strand	53	1	2
α-helix	57-67	11
β-strand	75-80	6	3
α-helix	86-92	7
β-strand	97-103	7	3
α-helix	111-113	3
β-strand	118	1	4
α-helix	121-123	3
β-strand	124-127	4	3
α-helix	136-137	2
β-strand	142-145	4	3
α-helix	154-173	20
β-strand	178-183	6	3
α-helix	189-202	14
β-strand	205-207	3	3
β-strand	219-222	4	3
α-helix	229-245	17
β-strand	252-253	2	1
α-helix	255-257	3
β-strand	258	1	2
β-strand	261	1	4
α-helix	275-288	14
β-strand	294	1	5
β-strand	305-313	9	5
β-strand	321-322	2	6
α-helix	323	1
α-helix	324-329	6
α-helix	331-333	3
α-helix	337-340	4
β-strand	342-344	3	7
β-strand	346	1	8
α-helix	349-355	7
α-helix	356-360	5
α-helix	364-368	5
α-helix	369-386	18
α-helix	394-396	3
α-helix	397-403	7
α-helix	423-426	4
α-helix	430-444	15
β-strand	453-457	5	5
α-helix	458	1
β-strand	461-463	3	7
α-helix	464	1
β-strand	465-466	2	9
β-strand	468	1	9
α-helix	469-470	2
β-strand	471	1	8
α-helix	472-473	2
β-strand	474-477	4	5
α-helix	480-490	11
α-helix	492-495	4
α-helix	501-504	4
β-strand	507	1	10
α-helix	513-525	13
β-strand	531	1	11
β-strand	532	1	10
α-helix	534-535	2
β-strand	536	1	12
α-helix	539-542	4
α-helix	545-551	7
α-helix	552-557	6
α-helix	560-568	9
α-helix	569-575	7
β-strand	579-584	6	5
β-strand	589-596	8	5
α-helix	607-627	21
α-helix	633-635	3
α-helix	641-660	20
β-strand	662-665	4	10
β-strand	668-671	4	10
α-helix	676-680	5
α-helix	683-687	5
α-helix	691	1
β-strand	692	1	12
α-helix	700-701	2
β-strand	704	1	11
α-helix	707-709	3
β-strand	712	1	13
β-strand	715	1	13
β-strand	716-721	6	14
β-strand	727-732	6	14
α-helix	735-742	8
β-strand	744-745	2	6
α-helix	752-769	18
α-helix	774-786	13
α-helix	791-793	3
α-helix	813-818	6
α-helix	819-823	5
α-helix	832-834	3
α-helix	837-839	3
α-helix	845-850	6
α-helix	858-878	21
α-helix	886-889	4
α-helix	891-893	3

Chain B: 57 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-28	8
β-strand	33-35	3	15
α-helix	38-45	8
β-strand	53	1	16
α-helix	57-67	11
β-strand	75-80	6	17
α-helix	86-92	7
β-strand	97-103	7	17
β-strand	118	1	18
α-helix	121-123	3
β-strand	124-127	4	17
α-helix	136-137	2
β-strand	142-145	4	17
α-helix	154-173	20
β-strand	178-183	6	17
α-helix	189-202	14
β-strand	205-207	3	17
β-strand	219-222	4	17
α-helix	229-245	17
β-strand	252-254	3	15
α-helix	255-257	3
β-strand	258	1	16
β-strand	261	1	18
α-helix	275-288	14
β-strand	294	1	19
β-strand	305-313	9	19
β-strand	321-322	2	20
α-helix	324-329	6
α-helix	331-333	3
α-helix	337-340	4
β-strand	342-344	3	21
β-strand	346	1	22
α-helix	349-355	7
α-helix	356-360	5
α-helix	364-368	5
α-helix	369-386	18
α-helix	394-396	3
α-helix	397-403	7
α-helix	423-427	5
α-helix	430-444	15
β-strand	453-457	5	19
α-helix	458	1
β-strand	461-463	3	21
α-helix	464	1
β-strand	465-466	2	23
β-strand	468	1	23
α-helix	469-470	2
β-strand	471	1	22
α-helix	472-473	2
β-strand	474-477	4	19
α-helix	480-490	11
α-helix	492-495	4
α-helix	501-504	4
β-strand	507	1	24
α-helix	513-525	13
β-strand	531	1	25
β-strand	532	1	24
α-helix	534-535	2
β-strand	536	1	26
α-helix	539-542	4
α-helix	545-551	7
α-helix	552-557	6
α-helix	560-568	9
α-helix	569-575	7
β-strand	579-584	6	19
α-helix	586-588	3
β-strand	589-596	8	19
α-helix	608-627	20
α-helix	633-635	3
α-helix	641-660	20
β-strand	662-665	4	24
β-strand	668-671	4	24
α-helix	676-680	5
α-helix	683-687	5
α-helix	691	1
β-strand	692	1	26
α-helix	699-701	3
β-strand	704	1	25
α-helix	707-709	3
β-strand	712	1	27
β-strand	715	1	27
β-strand	716-721	6	28
β-strand	727-732	6	28
α-helix	735-742	8
β-strand	744-745	2	20
α-helix	754-769	16
α-helix	774-786	13
α-helix	791-793	3
α-helix	813-817	5
α-helix	818-823	6
α-helix	832-834	3
α-helix	837-839	3
α-helix	845-850	6
α-helix	858-878	21
α-helix	886-889	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A, B	protein	905	Yellow fever virus 17D	P03314 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6QSN_1 Genome polyprotein (chains A, B)
GSANGKTLGEVWKRELNLLDKRQFELYKRTDIVEVDRDTARRHLAEGKVDTGVAVSRGTA
KLRWFHERGYVKLEGRVIDLGCGRGGWCYYAAAQKEVSGVKGFTLGRDGHEKPMNVQSLG
WNIITFKDKTDIHRLEPVKCDTLLCDIGESSSSSVTEGERTVRVLDTVEKWLACGVDNFC
VKVLAPYMPDVLEKLELLQRRFGGTVIRNPLSRNSTHEMYYVSGARSNVTFTVNQTSRLL
MRRMRRPTGKVTLEADVILPIGTRSVETDKGPLDKEAIEERVERIKSEYMTSWFYDNDNP
YRTWHYCGSYVTKTSGSAASMVNGVIKILTYPWDRIEEVTRMAMTDTTPFGQQRVFKEKV
DTRAKDPPAGTRKIMKVVNRWLFRHLAREKNPRLCTKEEFIAKVRSHAAIGAYLEEQEQW
KTANEAVQDPKFWELVDEERKLHQQGRCRTCVYNMMGKREKKLSEFGKAKGSRAIWYMWL
GARYLEFEALGFLNEDHWASRENSGGGVEGIGLQYLGYVIRDLAAMDGGGFYADDTAGWD
TRITEADLDDEQEILNYMSPHHKKLAQAVMEMTYKNKVVKVLRPAPGGKAYMDVISRRDQ
RGSGQVVTYALNTITNLKVQLIRMAEAEMVIHHQHVQDCDESVLTRLEAWLTEHGCDRLK
RMAVSGDDCVVRPIDDRFGLALSHLNAMSKVRKDISEWQPSKGWNDWENVPFCSHHFHEL
QLKDGRRIVVPCREQDELIGRGRVSPGNGWMIKETACLSKAYANMWSLMYFHKRDMRLLS
LAVSSAVPTSWVPQGRTTWSIHGKGEWMTTEDMLEVWNRVWITNNPHMQDKTMVKKWRDV
PYLTKRQDKLCGSLIGMTNRATWASHIHLVIHRIRTLIGQEKYTDYLTVMDRYSVDADLQ
LGELI

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Water and common crystallization additives (SO4) are not listed.

Primary citation

Structure of the yellow fever NS5 protein reveals conserved drug targets shared among flaviviruses. Dubankova, A., Boura, E. Antiviral Res (2019) 169:104536-104536. DOI 10.1016/j.antiviral.2019.104536 · PubMed

Other PDB entries of the same protein (UniProt P03314 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3EVF 1.45 Å, Crystal structure of Me7-GpppA complex of yellow fever virus methyltransferase and…
9SKO 1.49 Å, Crystal structure of HLA-A0201 in complex with peptide LLWNGPMAVS
3EVA 1.5 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
3EVD 1.5 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVC 1.6 Å, Crystal structure of GTP complex of yellow fever virus methyltransferase and…
3EVE 1.7 Å, Crystal structure of GpppA complex of yellow fever virus methyltransferase and…
5N6B 1.71 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNPGMAV
1YKS 1.8 Å, Crystal structure of yellow fever virus NS3 helicase
3EVB 1.85 Å, Crystal structure of yellow fever virus methyltransferase complexed with…
9SKP 1.89 Å, Crystal structure of HLA-A0201 in complex with peptide SLLWNGPMAV
6SSA 2.11 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPMQV
6SS8 2.24 Å, Human Leukocyte Antigen Class I A02 Carrying LLWNGPIAV

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