7CWC

Ambient-Temperature Serial Femtosecond X-ray Crystal structure of SARS-CoV-2 Main Protease at 2.1 A Resolution (P212121)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Near-physiological-temperature serial crystallography reveals conformations of SARS-CoV-2 main protease active site for improved drug repurposing.

Durdagi, S.Dag, C.Dogan, B.Yigin, M.Avsar, T.Buyukdag, C.Erol, I.Ertem, F.B.Calis, S.Yildirim, G.Orhan, M.D.Guven, O.Aksoydan, B.Destan, E.Sahin, K.Besler, S.O.Oktay, L.Shafiei, A.Tolu, I.Ayan, E.Yuksel, B.Peksen, A.B.Gocenler, O.Yucel, A.D.Can, O.Ozabrahamyan, S.Olkan, A.Erdemoglu, E.Aksit, F.Tanisali, G.Yefanov, O.M.Barty, A.Tolstikova, A.Ketawala, G.K.Botha, S.Dao, E.H.Hayes, B.Liang, M.Seaberg, M.H.Hunter, M.S.Batyuk, A.Mariani, V.Su, Z.Poitevin, F.Yoon, C.H.Kupitz, C.Sierra, R.G.Snell, E.H.DeMirci, H.

(2021) Structure 29: 1382-1396.e6

  • DOI: 10.1016/j.str.2021.07.007
  • Primary Citation of Related Structures:  
    7CWB, 7CWC

  • PubMed Abstract: 
  • The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments ...

    The COVID-19 pandemic has resulted in 198 million reported infections and more than 4 million deaths as of July 2021 (covid19.who.int). Research to identify effective therapies for COVID-19 includes: (1) designing a vaccine as future protection; (2) de novo drug discovery; and (3) identifying existing drugs to repurpose them as effective and immediate treatments. To assist in drug repurposing and design, we determine two apo structures of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) main protease at ambient temperature by serial femtosecond X-ray crystallography. We employ detailed molecular simulations of selected known main protease inhibitors with the structures and compare binding modes and energies. The combined structural and molecular modeling studies not only reveal the dynamics of small molecules targeting the main protease but also provide invaluable opportunities for drug repurposing and structure-based drug design strategies against SARS-CoV-2.


    Organizational Affiliation

    Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey; Stanford PULSE Institute, SLAC National Laboratory, Menlo Park, CA 94025, USA; Koc University Isbank Center for Infectious Diseases (KUISCID), 34450, Istanbul, Turkey. Electronic address: hdemirci@ku.edu.tr.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
3C-like proteinaseA, B310Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
Gene Names: rep1a-1b
EC: 3.4.22.69 (PDB Primary Data), 3.4.19.12 (UniProt), 3.4.22 (UniProt), 2.7.7.48 (UniProt), 3.6.4.12 (UniProt), 3.6.4.13 (UniProt), 3.1.13 (UniProt), 4.6.1 (UniProt), 2.1.1.57 (UniProt)
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
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.259 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.232 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 69.2α = 90
b = 104.3β = 90
c = 105.6γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
PDB_EXTRACTdata extraction
CrystFELdata reduction
CrystFELdata scaling

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data

  • Deposited Date: 2020-08-27 
  • Released Date: 2020-09-30 
  • Deposition Author(s): DeMirci, H.

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United StatesNSF-1231306
National Science Foundation (NSF, United States)Turkey118C260

Revision History  (Full details and data files)

  • Version 1.0: 2020-09-30
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Structure summary
  • Version 1.2: 2021-05-19
    Changes: Data collection
  • Version 1.3: 2021-12-15
    Changes: Database references