7T2T | pdb_00007t2t

SARS-CoV2 Mpro native form

• PDB DOI: https://doi.org/10.2210/pdb7T2T/pdb

• Classification: HYDROLASE
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2021-12-06 Released: 2022-09-14 
• Deposition Author(s): Mathews, I.I., Hameedi, M.A., Wakatsuki, S.
• Funding Organization(s): Department of Energy (DOE, United States)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free: 
  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 
  0.157 (Depositor) 

Starting Model: experimental

Literature

Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro.

Hameedi, M.A., T Prates, E., Garvin, M.R., Mathews, I.I., Amos, B.K., Demerdash, O., Bechthold, M., Iyer, M., Rahighi, S., Kneller, D.W., Kovalevsky, A., Irle, S., Vuong, V.Q., Mitchell, J.C., Labbe, A., Galanie, S., Wakatsuki, S., Jacobson, D.

(2022) Nat Commun 13: 5285-5285

• PubMed: 36075915 
• DOI: https://doi.org/10.1038/s41467-022-32922-9
• Primary Citation Related Structures: 
  7T2T, 7T2U, 7T2V


• PubMed Abstract: 
  

  In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO _226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.

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Organizational Affiliation: 
• SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA.
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA.
Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA.
National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Department of Horticulture, University of Kentucky, Lexington, KY, USA.
Chapman University School of Pharmacy, Irvine, CA, 92618, USA.
Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA.
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA. [e-mail].
SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA. [e-mail].
Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA. [e-mail].
National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA. [e-mail].
National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA. [e-mail].
Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global 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: 33.83 kDa 
• Atom Count: 2,630 
• Modeled Residue Count: 305 
• Deposited Residue Count: 306 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
3C-like proteinase	A	306	Severe acute respiratory syndrome coronavirus 2	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.45 Å
• R-Value Free:  0.200 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.155 (Depositor), 0.161 (DCC) 
• R-Value Observed: 0.157 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 114.17	α = 90
b = 53.44	β = 103.02
c = 44.87	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-09-14 
Deposition Author(s): Mathews, I.I., Hameedi, M.A., Wakatsuki, S.

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Funding Organization	Location	Grant Number
Department of Energy (DOE, United States)	United States	DE-AC02-76SF00515

Revision History  

• Version 1.0: 2022-09-14
  Type: Initial release
  
• Version 1.1: 2022-09-21
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description