5GOZ: ZIKV NS5 Methyltransferase

Name: PDB 5GOZ: Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH
Published: 2016-12-07
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: transferase

Crystal structure of ZIKV NS5 Methyltransferase in complex with GTP and SAH. Determined by X-ray diffraction at 2.05 Å resolution. Released 7 Dec 2016.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Zika virus (strain Mr 766)
Chains: 3
Atoms: 6,543
Mol. weight: 93.39 kDa
Ligands: PO4, SIN, POP, SAH
Released: 7 Dec 2016

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

Secondary structure: helices and β-sheets

5GOZ contains 37 α-helices and 31 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: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	21-27	7
β-strand	33-35	3	1
α-helix	38-46	9
β-strand	53	1	2
α-helix	58-66	9
β-strand	75-80	6	3
α-helix	86-91	6
β-strand	97-103	7	3
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	3
α-helix	132-134	3
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	252-254	3	1
α-helix	255-257	3
β-strand	258	1	2

Chain B: 12 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	21-28	8
β-strand	33-35	3	4
α-helix	38-41	4
α-helix	58-66	9
β-strand	75-80	6	5
α-helix	86-91	6
β-strand	97-103	7	5
β-strand	126-127	2	5
α-helix	132-134	3
α-helix	136-137	2
β-strand	142-145	4	5
α-helix	154-173	20
β-strand	178-183	6	5
α-helix	189-202	14
β-strand	205-207	3	5
β-strand	219-222	4	5
α-helix	229-244	16
α-helix	248-251	4
β-strand	252-254	3	4
α-helix	255-257	3

Chain C: 13 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9
α-helix	21-27	7
β-strand	33-36	4	6
α-helix	38-44	7
β-strand	53	1	7
α-helix	58-66	9
β-strand	75-80	6	8
α-helix	86-91	6
β-strand	97-103	7	8
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	8
α-helix	132-134	3
β-strand	142-145	4	8
α-helix	154-172	19
β-strand	178-183	6	8
α-helix	189-202	14
β-strand	205-207	3	8
β-strand	219-222	4	8
α-helix	229-245	17
α-helix	247-248	2
β-strand	252-255	4	6
α-helix	256-257	2
β-strand	258	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
RNA-directed RNA polymerase NS5	A, B, C	protein	269	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>5GOZ_1 RNA-directed RNA polymerase NS5 (chains A, B, C)
GSVDTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGS
AKLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPMLVQSY
GWNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAF
CIKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQL
LLGRMDGPRRPVKYEEDVNLGSGTRAAAS

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	5
SIN	Succinic acid	C4 H6 O4	3
POP	Pyrophosphate 2-	H2 O7 P2	1
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	3
GTP	Guanosine-5'-triphosphate	C10 H16 N5 O14 P3	4

Primary citation

Structure of the NS5 methyltransferase from Zika virus and implications in inhibitor design. Zhang, C., Feng, T., Cheng, J. et al. Biochem Biophys Res Commun (2017) 492:624-630. DOI 10.1016/j.bbrc.2016.11.098 · PubMed

Other PDB entries of the same protein (UniProt A0A024B7W1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5KQR 1.33 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine
6LD1 1.4 Å, Zika NS5 polymerase domain
6LD2 1.4 Å, Zika NS5 polymerase domain
5KQS 1.5 Å, Structure of NS5 methyltransferase from Zika virus bound to S-adenosylmethionine and…
6LD4 1.5 Å, Zika NS5 polymerase domain
6S0J 1.5 Å, Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-
5ULP 1.55 Å, Structure of the NS5 methyltransferase from Zika bound to MS2042
5Y6N 1.57 Å, Zika virus helicase in complex with ADP
7M1V 1.6 Å, Structure of Zika virus NS2b-NS3 protease mutant binding the compound NSC86314 in the…
5KVE 1.7 Å, Zika specific antibody, ZV-48, bound to ZIKA envelope DIII
6RWZ 1.7 Å, Structure of Zika virus NS3 helicase in complex with ADP-BeF3
5JMT 1.8 Å, Crystal structure of Zika virus NS3 helicase

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