6S0J: Zika virus NS3 helicase

Structure of Zika virus NS3 helicase in complex with ADP-MgF3(H2O)-. Determined by X-ray diffraction at 1.5 Å resolution. Released 15 Jul 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Zika virus (strain Mr 766)
Chains: 1
Atoms: 3,935
Mol. weight: 51.29 kDa
Ligands: ADP, MG, KQB
Released: 15 Jul 2020

Explore 6S0J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6S0J contains 22 α-helices and 21 β-strands across 1 chain. 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: 22 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	189-192	4	1
α-helix	194-195	2
α-helix	200-204	5
α-helix	205-215	11
β-strand	219-223	5	1
α-helix	226-235	10
β-strand	241-243	3	1
β-strand	258-262	5	1
α-helix	263-271	9
β-strand	281-285	5	1
α-helix	292-306	15
β-strand	311-315	5	1
β-strand	333-337	5	2
α-helix	350-353	4
β-strand	359-362	4	2
α-helix	366-378	13
β-strand	383-386	4	2
α-helix	391-400	10
β-strand	405-408	4	2
α-helix	410-413	4
β-strand	422-425	4	2
β-strand	428-435	8	3
β-strand	439-447	9	3
α-helix	448-449	2
α-helix	450-457	8
β-strand	469-473	5	2
α-helix	486-494	9
β-strand	500	1	4
β-strand	503	1	4
α-helix	505-508	4
α-helix	509-514	6
α-helix	523-525	3
α-helix	526-537	12
α-helix	543-551	9
α-helix	560-562	3
α-helix	567-569	3
β-strand	572-573	2	5
β-strand	576-577	2	5
β-strand	579-581	3	6
β-strand	587-589	3	6
β-strand	596	1	3
α-helix	597-599	3
α-helix	603-613	11

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A	protein	451	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6S0J_1 Genome polyprotein (chains A)
MGSSHHHHHHMLKKKQLTVLDLHPGAGKTRRVLPEIVREAIKTRLRTVILAPTRVVAAEM
EEALRGLPVRYMTTAVNVTHSGTEIVDLMCHATFTSRLLQPIRVPNYNLYIMDEAHFTDP
SSIAARGYISTRVEMGEAAAIFMTATPPGTRDAFPDSNSPIMDTEVEVPERAWSSGFDWV
TDYSGKTVWFVPSVRNGNEIAACLTKAGKRVIQLSRKTFETEFQKTKHQEWDFVVTTDIS
EMGANFKADRVIDSRRCLKPVILDGERVILAGPMPVTHASAAQRRGRIGRNPNKPGDEYL
YGGGCAETDEDHAHWLEARMLLDNIYLQDGLIASLYRPEADKVAAIEGEFKLRTEQRKTF
VELMKRGDLPVWLAYQVASAGITYTDRRWCFDGTTNNTIMEDSVPAEVWTRHGEKRVLKP
RWMDARVCSDHAALKSFKEFAAGKRGAAFGV

Ligands and cofactors

ID	Name	Formula	Copies
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	1
MG	Magnesium ion	Mg	1
KQB	trifluoromagnesate monohydrate	F3 H2 Mg O	1

Primary citation

Octahedral Trifluoromagnesate, an Anomalous Metal Fluoride Species, Stabilizes the Transition State in a Biological Motor. Ge, M., Molt Jr., R.W., Jenkins, H.T. et al. ACS Catal (2021) 11:2769-2773. DOI 10.1021/acscatal.0c04500 · 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
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
5MRK 1.9 Å, Structural basis of Zika virus methyltransferase inhibition by sinefungin

Browse structure collections

About this viewer

MolViewer shows 6S0J 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.