5ULP: NS5 methyltransferase from Zika

Structure of the NS5 methyltransferase from Zika bound to MS2042. Determined by X-ray diffraction at 1.55 Å resolution. Released 17 May 2017.

Method: X-ray diffraction
Resolution: 1.55 Å
Organism: Zika virus (strain Mr 766)
Chains: 2
Atoms: 4,894
Mol. weight: 60.84 kDa
Ligands: IPA, URE, KB1
Released: 17 May 2017

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

Secondary structure: helices and β-sheets

5ULP contains 24 α-helices and 20 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: 12 helices, 9 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
α-helix	58-67	10
β-strand	75-80	6	2
α-helix	86-91	6
β-strand	97-103	7	2
α-helix	111-113	3
α-helix	121-123	3
β-strand	124-127	4	2
α-helix	132-134	3
β-strand	142-145	4	2
α-helix	154-172	19
β-strand	178-183	6	2
α-helix	189-202	14
β-strand	205-207	3	2
β-strand	219-222	4	2
α-helix	229-242	14
α-helix	248-251	4
β-strand	252-253	2	1

Chain B: 12 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	8-17	10
α-helix	21-28	8
β-strand	33-34	2	3
α-helix	38-45	8
β-strand	53	1	4
α-helix	58-67	10
β-strand	75-80	6	5
α-helix	86-92	7
β-strand	97-103	7	5
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	5
α-helix	132-134	3
β-strand	142-145	4	5
α-helix	154-172	19
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	229-242	14
α-helix	250-251	2
β-strand	252-253	2	3
β-strand	258	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
MRNA cap 0-1 NS5-type methyltransferase	A, B	protein	268	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5ULP_1 MRNA cap 0-1 NS5-type methyltransferase (chains A, B)
GGGTGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSA
KLRWLVERGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPMLVQSYG
WNIVRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFC
IKVLCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLL
LGRMDGPRRPVKYEEDVNLGSGTRAVVS

Ligands and cofactors

ID	Name	Formula	Copies
IPA	Isopropyl alcohol	C3 H8 O	1
URE	Urea	C H4 N2 O	8
KB1	5'-{[(3S)-3-amino-3-carboxypropyl][(4-fluorophenyl)methyl]amino}-5'-deoxyadenos…	C21 H26 F N7 O5	2

Water and common crystallization additives (NA, CL) are not listed.

Primary citation

Development of a S-adenosylmethionine analog that intrudes the RNA-cap binding site of Zika methyltransferase. Jain, R., Butler, K.V., Coloma, J. et al. Sci Rep (2017) 7:1632-1632. DOI 10.1038/s41598-017-01756-7 · 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)-
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
5MRK 1.9 Å, Structural basis of Zika virus methyltransferase inhibition by sinefungin

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