5NJU: Flavivirus NS5 domain

Flavivirus NS5 domain. Determined by X-ray diffraction at 2.1 Å resolution. Released 24 Jan 2018.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Zika virus
Chains: 2
Atoms: 4,461
Mol. weight: 58.63 kDa
Ligands: MG, SAH
Released: 24 Jan 2018

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

Secondary structure: helices and β-sheets

5NJU contains 26 α-helices and 22 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: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-28	8
β-strand	33-35	3	1
α-helix	41-46	6
β-strand	53	1	2
α-helix	58-67	10
β-strand	75-80	6	3
α-helix	86-91	6
β-strand	97-103	7	3
α-helix	111-115	5
α-helix	121-123	3
β-strand	124-127	4	3
α-helix	132-134	3
β-strand	135	1	4
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	229-242	14
β-strand	252-254	3	1
α-helix	255-257	3
β-strand	258	1	2

Chain B: 13 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-28	8
β-strand	33-35	3	5
α-helix	58-67	10
β-strand	75-80	6	6
α-helix	86-91	6
β-strand	97-103	7	6
α-helix	111-115	5
α-helix	121-123	3
β-strand	124-127	4	6
α-helix	132-134	3
α-helix	136-139	4
β-strand	142-145	4	6
α-helix	154-172	19
β-strand	178-183	6	6
α-helix	189-202	14
β-strand	205-207	3	6
β-strand	219-222	4	6
β-strand	225	1	4
α-helix	226-227	2
α-helix	229-242	14
α-helix	248-251	4
β-strand	252-254	3	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Genome polyprotein	A, B	protein	260	Zika virus	A0A024B7W1 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>5NJU_1 Genome polyprotein (chains A, B)
GETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLRW
LVDRGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNIV
RLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKVL
CPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGRM
DGPRRPVKYEEDVNLGSGTR

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

Primary citation

The structure of the binary methyltransferase-SAH complex from Zika virus reveals a novel conformation for the mechanism of mRNA capping. Chatrin, C., Talapatra, S.K., Canard, B. et al. Oncotarget (2018) 9:3160-3171. DOI 10.18632/oncotarget.23223 · 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

Browse structure collections

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