9FEH: SARS-CoV-2 nsp14 methyltransferase domain

Crystal structure of SARS-CoV-2 nsp14 methyltransferase domain in complex with the STM957 inhibitor. Determined by X-ray diffraction at 1.99 Å resolution. Released 28 Aug 2024.

Method: X-ray diffraction
Resolution: 1.99 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 2,322
Mol. weight: 36.18 kDa
Ligands: ZN, A1IB6
Released: 28 Aug 2024

Explore 9FEH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9FEH contains 17 α-helices and 9 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: 17 helices, 9 β-strands

Element	Residues	Length	Sheet
α-helix	231-233	3
α-helix	236-249	14
α-helix	252-254	3
α-helix	257-260	4
α-helix	264-267	4
α-helix	272-278	7
α-helix	283-295	13
α-helix	297-301	5
α-helix	302-324	23
β-strand	328-332	5	1
β-strand	347-352	6	1
α-helix	360-362	3
β-strand	364-365	2	1
α-helix	370-373	4
β-strand	381-385	5	1
β-strand	396-400	5	1
α-helix	434-436	3
β-strand	440-441	2	1
β-strand	446-447	2	2
α-helix	451-452	2
β-strand	473-474	2	2
α-helix	476-478	3
α-helix	485-503	19
β-strand	507-510	4	1
α-helix	517-520	4
α-helix	521-523	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor ETV6,Guanine-N7 methyltransferase nsp14	A	protein	308	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model), P41212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9FEH_1 Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 (chains A)
SIRLPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYRS
PHSGDELYELLQHILKQPAAGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAIK
CVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIVC
RFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQV
VSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYNL
WNTFTRLQ

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
A1IB6	~{N}-[[(2~{R},3~{S},4~{R},5~{R})-5-[4-azanyl-5-(2-pyridin-3-ylethynyl)pyrrolo[2…	C28 H27 N7 O6 S	1

Primary citation

Structure of SARS-CoV-2 MTase nsp14 with the inhibitor STM957 reveals inhibition mechanism that is shared with a poxviral MTase VP39. Zilecka, E., Klima, M., Stefek, M. et al. J Struct Biol X (2024) 10:100109-100109. DOI 10.1016/j.yjsbx.2024.100109 · PubMed

Other PDB entries of the same protein (UniProt P0DTD1 (AlphaFold model), which also has an AlphaFold model), best resolution first:

44PS 0.77 Å, 6-conformation model of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
7KR0 0.77 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (C2 crystal form, 100 K)
9CY0 0.8 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with AVI-4206
7TX0 0.84 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose at pH 9 (P43…
7KQO 0.85 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain (P43 crystal form)
7HCO 0.87 Å, PanDDA analysis group deposition -- Crystal structure of SARS-CoV-2 NSP3 macrodomain in…
7KQP 0.88 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain in complex with ADP-ribose (P43 crystal…
7TWJ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 4 (P43 crystal form)
7TWN 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 5 (P43 crystal form)
7TWO 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 6 (P43 crystal form)
7TWP 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 7 (P43 crystal form)
7TWQ 0.9 Å, Crystal structure of SARS-CoV-2 NSP3 macrodomain at pH 9 (P43 crystal form)

Browse structure collections

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