6X42

High Resolution Crystal Structure Analysis of SERA5E from plasmodium falciparum


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure of the Plasmodium falciparum PfSERA5 pseudo-zymogen.

Smith, N.A.Clarke, O.B.Lee, M.Hodder, A.N.Smith, B.J.

(2020) Protein Sci 29: 2245-2258

  • DOI: https://doi.org/10.1002/pro.3956
  • Primary Citation of Related Structures:  
    6X42, 6X44

  • PubMed Abstract: 

    PfSERA5, a significantly abundant protein present within the parasitophorous vacuole (PV) and essential for normal growth during the blood-stage life cycle of the malaria parasite Plasmodium falciparum, displays structural similarity to many other cysteine proteases. However, PfSERA5 does not exhibit any detectable protease activity and therefore the role of the PfSERA5 papain-like domain (PfSERA5E), thought to remain bound to its cognate prodomain, remains unknown. In this study, we present a revised structure of the central PfSERA5E domain at a resolution of 1.2 Å, and the first structure of the "zymogen" of this papain-like domain including its cognate prodomain (PfSERA5PE) to 2.2 Å resolution. PfSERA5PE is somewhat structurally similar to that of other known proenzymes, retaining the conserved overall folding and orientation of the prodomain through, and occluding, the archetypal papain-like catalytic triad "active-site" cleft, in the same reverse direction as conventional prodomains. Our findings are congruent with previously identified structures of PfSERA5E and of similar "zymogens" and provide a foundation for further investigation into the function of PfSERA5.


  • Organizational Affiliation

    Department of Chemistry and Physics, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, Australia.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine repeat antigen 5A [auth X]285Plasmodium falciparumMutation(s): 0 
Gene Names: sera5
UniProt
Find proteins for Q9TY95 (Plasmodium falciparum (isolate 3D7))
Explore Q9TY95 
Go to UniProtKB:  Q9TY95
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9TY95
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.147 
  • R-Value Work: 0.126 
  • R-Value Observed: 0.127 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.288α = 90
b = 102.288β = 90
c = 71.718γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
Cootmodel building
PHASERphasing
XDSdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-10-07
    Type: Initial release
  • Version 1.1: 2020-11-04
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Database references, Refinement description