7T2U

SARS-CoV2 3C-Like protease complexed with Nemo peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


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

  • DOI: https://doi.org/10.1038/s41467-022-32922-9
  • Primary Citation of 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.


  • Organizational Affiliation

    SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
3C-Like ProteaseA,
B,
D [auth C],
F [auth D]
319Severe acute respiratory syndrome coronavirus 2Mutation(s): 1 
Gene Names: rep1a-1b
EC: 3.4.22.69
UniProt
Find proteins for P0DTD1 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTD1 
Go to UniProtKB:  P0DTD1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0DTD1
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NEMO peptideC [auth E],
E [auth F]
10Homo sapiensMutation(s): 0 
Gene Names: IKBKGFIP3NEMO
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K9 (Homo sapiens)
Explore Q9Y6K9 
Go to UniProtKB:  Q9Y6K9
PHAROS:  Q9Y6K9
GTEx:  ENSG00000269335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6K9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.300 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.248 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.39α = 102.51
b = 67.71β = 89.91
c = 77.84γ = 107.39
Software Package:
Software NamePurpose
REFMACrefinement
XSCALEdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Department of Energy (DOE, United States)United StatesDE-AC02-76SF00515

Revision History  (Full details and data files)

  • Version 1.0: 2022-09-14
    Type: Initial release
  • Version 1.1: 2022-09-21
    Changes: Database references
  • Version 1.2: 2024-04-03
    Changes: Data collection, Refinement description