8P61 | pdb_00008p61

Crystal structure of O'nyong'nyong virus capsid protease (106-256)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.230 (DCC) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Autoinhibition of suicidal capsid protease from O'nyong'nyong virus.

Chykunova, Y.Plewka, J.Wilk, P.Sienczyk, M.Dubin, G.Pyrc, K.

(2024) Int J Biol Macromol 262: 130136-130136

  • DOI: https://doi.org/10.1016/j.ijbiomac.2024.130136
  • Primary Citation of Related Structures:  
    8P61

  • PubMed Abstract: 

    Alphaviruses pose a significant threat to public health. Capsid protein encoded in the alphaviral genomes constitutes an interesting therapy target, as it also serves as a protease (CP). Remarkably, it undergoes autoproteolysis, leading to the generation of the C-terminal tryptophan that localizes to the active pocket, deactivating the enzyme. Lack of activity hampers the viral replication cycle, as the virus is not capable of producing the infectious progeny. We investigated the structure and function of the CP encoded in the genome of O'nyong'nyong virus (ONNV), which has instigated outbreaks in Africa. Our research provides a high-resolution crystal structure of the ONNV CP in its active state and evaluates the enzyme's activity. Furthermore, we demonstrated a dose-dependent reduction in ONNV CP proteolytic activity when exposed to indole, suggesting that tryptophan analogs may be a promising basis for developing small molecule inhibitors. It's noteworthy that the capsid protease plays an essential role in virus assembly, binding viral glycoproteins through its glycoprotein-binding hydrophobic pocket. We showed that non-aromatic cyclic compounds like dioxane disrupt this vital interaction. Our findings provide deeper insights into ONNV's biology, and we believe they will prove instrumental in guiding the development of antiviral strategies against arthritogenic alphaviruses.


  • Organizational Affiliation

    Virogenetics Laboratory of Virology, Malopolska Centre of Biotechnology, Jagiellonian University, Gronostajowa 7a, 30-387 Krakow, Poland; Department of Microbiology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa 7, 30-387 Krakow, Poland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Capsid protein
A, B, C, D
153O'nyong-nyong virus strain GuluMutation(s): 0 
EC: 3.4.21.90
UniProt
Find proteins for P22056 (O'nyong-nyong virus (strain Gulu))
Explore P22056 
Go to UniProtKB:  P22056
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP22056
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
J [auth B]
L [auth C]
M [auth C]
F [auth A],
G [auth A],
J [auth B],
L [auth C],
M [auth C],
N [auth C],
O [auth C],
P [auth C],
Q [auth D],
R [auth D],
S [auth D],
T [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
I [auth B],
K [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.268 (Depositor), 0.270 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.230 (DCC) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.65α = 90
b = 112.13β = 89.97
c = 67.1γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Polish National Science CentrePolandUMO-2017/27/B/NZ6/02488

Revision History  (Full details and data files)

  • Version 1.0: 2024-03-06
    Type: Initial release
  • Version 2.0: 2024-05-15
    Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary