8FRK: PDB entry 8FRK

Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to SGC8158. Determined by X-ray diffraction at 1.61 Å resolution. Released 26 Jul 2023.

Method: X-ray diffraction
Resolution: 1.61 Å
Organism: Severe acute respiratory syndrome coronavirus 2
Chains: 1
Atoms: 2,361
Mol. weight: 36.14 kDa
Ligands: MJ7, EOH, ZN
Released: 26 Jul 2023

Explore 8FRK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8FRK 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	8-10	3
α-helix	13-15	3
α-helix	18-31	14
α-helix	34-36	3
α-helix	39-42	4
α-helix	46-49	4
α-helix	54-60	7
α-helix	65-77	13
α-helix	79-301	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	396-401	6	1
α-helix	434-436	3
β-strand	439-441	3	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	506-511	6	1
α-helix	517-520	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera	A	protein	309	Severe acute respiratory syndrome coronavirus 2	P0DTD1 (AlphaFold model), P41212 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8FRK_1 Transcription factor ETV6,Guanine-N7 methyltransferase nsp14 chimera (chains A)
GSIALPAHLRLQPIYWSRDDVAQWLKWAENEFSLRPIDSNTFEMNGKALLLLTKEDFRYR
SPHSGDELYELLQHILAQPAAGDELKINAACRKVQHMVVKAALLADKFPVLHDIGNPKAI
KCVPQADVEWKFYDAQPCSDKAYKIEELFYSYATHSDKFTDGVCLFWNCNVDRYPANSIV
CRFDTRVLSNLNLPGCDGGSLYVNKHAFHTPAFDKSAFVNLKQLPFFYYSDSPCESHGKQ
VVSDIDYVPLKSATCITRCNLGGAVCRHHANEYRLYLDAYNMMISAGFSLWVYKQFDTYN
LWNTFTRLQ

Ligands and cofactors

ID	Name	Formula	Copies
MJ7	5'-S-(4-{[(4'-chloro[1,1'-biphenyl]-3-yl)methyl]amino}butyl)-5'-thioadenosine	C27 H31 Cl N6 O3 S	1
EOH	Ethanol	C2 H6 O	1
ZN	Zinc ion	Zn	1

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

Primary citation

Structures of SARS-CoV-2 N7-methyltransferase with DOT1L and PRMT7 inhibitors provide a platform for new antivirals. Kottur, J., White, K.M., Rodriguez, M.L. et al. PLoS Pathog (2023) 19:e1011546-e1011546. DOI 10.1371/journal.ppat.1011546 · 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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