3D23

Main protease of HCoV-HKU1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure of the main protease from a global infectious human coronavirus, HCoV-HKU1.

Zhao, Q.Li, S.Xue, F.Zou, Y.Chen, C.Bartlam, M.Rao, Z.

(2008) J.Virol. 82: 8647-8655

  • DOI: 10.1128/JVI.00298-08

  • PubMed Abstract: 
  • The newly emergent human coronavirus HKU1 (HCoV-HKU1) was first identified in Hong Kong in 2005. Infection by HCoV-HKU1 occurs worldwide and causes syndromes such as the common cold, bronchitis, and pneumonia. The CoV main protease (M(pro)), which is ...

    The newly emergent human coronavirus HKU1 (HCoV-HKU1) was first identified in Hong Kong in 2005. Infection by HCoV-HKU1 occurs worldwide and causes syndromes such as the common cold, bronchitis, and pneumonia. The CoV main protease (M(pro)), which is a key enzyme in viral replication via the proteolytic processing of the replicase polyproteins, has been recognized as an attractive target for rational drug design. In this study, we report the structure of HCoV-HKU1 M(pro) in complex with a Michael acceptor, inhibitor N3. The structure of HCoV-HKU1 provides a high-quality model for group 2A CoVs, which are distinct from group 2B CoVs such as severe acute respiratory syndrome CoV. The structure, together with activity assays, supports the relative conservation at the P1 position that was discovered by sequencing the HCoV-HKU1 genome. Combined with structural data from other CoV M(pro)s, the HCoV-HKU1 M(pro) structure reported here provides insights into both substrate preference and the design of antivirals targeting CoVs.


    Organizational Affiliation

    Tsinghua-Nankai-IBP Joint Research Group for Structural Biology, Tsinghua University, Beijing, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
3C-like proteinase
B, A, C, D
302Human coronavirus HKU1Mutation(s): 0 
Find proteins for P0C6U3 (Human coronavirus HKU1)
Go to UniProtKB:  P0C6U3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
N-[(5-METHYLISOXAZOL-3-YL)CARBONYL]ALANYL-L-VALYL-N~1~-((1R,2Z)-4-(BENZYLOXY)-4-OXO-1-{[(3R)-2-OXOPYRROLIDIN-3-YL]METHYL}BUT-2-ENYL)-L-LEUCINAMIDE
H, F, E, G
6N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.285 
  • R-Value Work: 0.229 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 91.770α = 90.00
b = 91.770β = 90.00
c = 187.914γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
PDB_EXTRACTdata extraction
REFMACrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-09-16
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Source and taxonomy, Version format compliance
  • Version 1.2: 2015-12-09
    Type: Derived calculations, Structure summary
  • Version 1.3: 2017-10-25
    Type: Refinement description