7TW9

Structure of nsp14 N7-MethylTransferase domain fused with TELSAM bound to Sinefungin

• PDB DOI: https://doi.org/10.2210/pdb7TW9/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2022-02-06 Released: 2022-09-07 
• Deposition Author(s): Kottur, J., Aggarwal, A.K.
• Funding Organization(s): Not funded

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.232 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Starting Models: experimental

Literature

High-resolution structures of the SARS-CoV-2 N7-methyltransferase inform therapeutic development.

Kottur, J., Rechkoblit, O., Quintana-Feliciano, R., Sciaky, D., Aggarwal, A.K.

(2022) Nat Struct Mol Biol 29: 850-853

• PubMed: 36075969 
• DOI: https://doi.org/10.1038/s41594-022-00828-1
• Primary Citation of Related Structures:  
  7TW7, 7TW8, 7TW9


• PubMed Abstract: 
  

  Emergence of SARS-CoV-2 coronavirus has led to millions of deaths globally. We present three high-resolution crystal structures of the SARS-CoV-2 nsp14 N7-methyltransferase core bound to S-adenosylmethionine (1.62 Å), S-adenosylhomocysteine (1.55 Å) and sinefungin (1.41 Å). We identify features of the methyltransferase core that are crucial for the development of antivirals and show SAH as the best scaffold for the design of antivirals against SARS-CoV-2 and other pathogenic coronaviruses.

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Organizational Affiliation: 

Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 36.2 kDa 
• Atom Count: 2,569 
• Modelled Residue Count: 261 
• Deposited Residue Count: 309 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Transcription factor ETV6,Proofreading exoribonuclease nsp14 chimera	A	309	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 3  Gene Names: ETV6, TEL, TEL1, rep, 1a-1b EC: 3.1.13
UniProt & NIH Common Fund Data Resources
Find proteins for P41212 (Homo sapiens) Explore P41212  Go to UniProtKB:  P41212
PHAROS:  P41212 GTEx:  ENSG00000139083
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1
UniProt Groups	P0DTD1P41212

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SFG (Subject of Investigation/LOI)	B [auth A]	SINEFUNGIN C15 H23 N7 O5 LMXOHSDXUQEUSF-YECHIGJVSA-N
PEG	D [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EOH	E [auth A]	ETHANOL C2 H6 O LFQSCWFLJHTTHZ-UHFFFAOYSA-N
MOH	F [auth A], G [auth A], H [auth A], I [auth A], J [auth A]	METHANOL C H4 O OKKJLVBELUTLKV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.41 Å
• R-Value Free: 0.232 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 6₅

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.028	α = 90
b = 109.028	β = 90
c = 48.641	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
STARANISO	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-09-07 
Deposition Author(s): Kottur, J., Aggarwal, A.K.

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Funding Organization	Location	Grant Number
Not funded		--

Revision History  

• Version 1.0: 2022-09-07
  Type: Initial release
  
• Version 1.1: 2022-09-21
  Changes: Database references
• Version 1.2: 2022-10-05
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description