5NJV: Flavivirus NS5 domain

Flavivirus NS5 domain. Determined by X-ray diffraction at 2.0 Å resolution. Released 24 Jan 2018.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: Zika virus (strain Mr 766)
Chains: 4
Atoms: 8,667
Mol. weight: 118.05 kDa
Ligands: SAM
Released: 24 Jan 2018

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

Secondary structure: helices and β-sheets

5NJV contains 54 α-helices and 42 β-strands across 4 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, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-27	7
β-strand	33-35	3	1
α-helix	38-46	9
α-helix	58-67	10
β-strand	75-80	6	2
α-helix	86-92	7
β-strand	97-103	7	2
α-helix	121-123	3
β-strand	124-127	4	2
α-helix	132-134	3
α-helix	136-137	2
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	229-245	17
α-helix	247-251	5
β-strand	252-254	3	1
α-helix	255-257	3

Chain B: 14 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	21-29	9
β-strand	33-35	3	3
α-helix	38-46	9
α-helix	58-66	9
β-strand	75-80	6	4
α-helix	86-92	7
β-strand	97-103	7	4
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	4
α-helix	136-137	2
β-strand	142-145	4	4
α-helix	154-172	19
β-strand	178-183	6	4
α-helix	189-202	14
β-strand	205-207	3	4
β-strand	219-222	4	4
α-helix	229-245	17
α-helix	247-248	2
α-helix	250-251	2
β-strand	252-254	3	3
α-helix	255-257	3

Chain C: 13 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-16	9
β-strand	20	1	5
α-helix	21-28	8
β-strand	33-35	3	6
α-helix	38-41	4
β-strand	53	1	7
α-helix	58-67	10
β-strand	75-80	6	8
α-helix	86-91	6
β-strand	97-103	7	8
α-helix	121-123	3
β-strand	124-127	4	8
α-helix	132-134	3
α-helix	136-137	2
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	229-242	14
α-helix	249-251	3
β-strand	252-254	3	6
α-helix	255-257	3
β-strand	258	1	7

Chain D: 14 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
β-strand	20	1	5
α-helix	21-27	7
β-strand	33-36	4	9
α-helix	38-41	4
β-strand	53	1	10
α-helix	58-67	10
β-strand	75-80	6	11
α-helix	86-91	6
β-strand	97-103	7	11
α-helix	111-114	4
α-helix	121-123	3
β-strand	124-127	4	11
α-helix	132-134	3
α-helix	136-137	2
β-strand	142-145	4	11
α-helix	154-172	19
β-strand	178-183	6	11
α-helix	189-202	14
β-strand	205-207	3	11
β-strand	219-222	4	11
α-helix	229-245	17
α-helix	247-251	5
β-strand	252-255	4	9
α-helix	256-257	2
β-strand	258	1	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
NS5	A, B, C, D	protein	262	Zika virus (strain Mr 766)	A0A024B7W1 (AlphaFold model)

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

>5NJV_1 NS5 (chains A, B, C, D)
TGETLGEKWKARLNQMSALEFYSYKKSGITEVCREEARRALKDGVATGGHAVSRGSAKLR
WLVDRGYLQPYGKVIDLGCGRGGWSYYAATIRKVQEVKGYTKGGPGHEEPVLVQSYGWNI
VRLKSGVDVFHMAAEPCDTLLCDIGESSSSPEVEEARTLRVLSMVGDWLEKRPGAFCIKV
LCPYTSTMMETLERLQRRYGGGLVRVPLSRNSTHEMYWVSGAKSNTIKSVSTTSQLLLGR
MDGPRRPVKYEEDVNLGSGTRA

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	4

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

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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