8D35

Crystal structure of SARS-CoV-2 main protease (Mpro) C145A mutant in complex with peptide from human tRNA methyltransferase TRMT1

• PDB DOI: https://doi.org/10.2210/pdb8D35/pdb

• Classification: VIRAL PROTEIN, HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2, Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2022-05-31 Released: 2023-03-01 
• Deposition Author(s): D'Oliviera, A., Mugridge, J.S.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Recognition and Cleavage of Human tRNA Methyltransferase TRMT1 by the SARS-CoV-2 Main Protease.

D'Oliviera, A., Dai, X., Mottaghinia, S., Geissler, E.P., Etienne, L., Zhang, Y., Mugridge, J.S.

(2023) Elife 

• DOI: https://doi.org/10.7554/eLife.91168.1

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 69.58 kDa 
• Atom Count: 5,099 
• Modelled Residue Count: 609 
• Deposited Residue Count: 627 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase nsp5	A, B	308	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 1  Gene Names: rep, 1a-1b EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTD1  Go to UniProtKB:  P0DTD1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
tRNA (guanine(26)-N(2))-dimethyltransferase	C	11	Homo sapiens	Mutation(s): 0  EC: 2.1.1.216
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NXH9 (Homo sapiens) Explore Q9NXH9  Go to UniProtKB:  Q9NXH9
PHAROS:  Q9NXH9 GTEx:  ENSG00000104907

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	F [auth A], H [auth B], I [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	E [auth A], G [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.224 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.787	α = 90
b = 100.029	β = 90
c = 103.252	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XDS	data scaling
PHASER	phasing
PHENIX	refinement
Coot	model building

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-03-01 
Deposition Author(s): D'Oliviera, A., Mugridge, J.S.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM143000

Revision History  

• Version 1.0: 2023-03-01
  Type: Initial release
  
• Version 1.1: 2023-03-08
  Changes: Database references
• Version 1.2: 2023-03-15
  Changes: Database references
• Version 1.3: 2023-10-25
  Changes: Data collection, Refinement description
• Version 1.4: 2023-11-22
  Changes: Database references, Structure summary