3PNR | pdb_00003pnr

Structure of PbICP-C in complex with falcipain-2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work: 
    0.181 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 
    0.183 (Depositor) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural basis for the regulation of cysteine-protease activity by a new class of protease inhibitors in Plasmodium.

Hansen, G.Heitmann, A.Witt, T.Li, H.Jiang, H.Shen, X.Heussler, V.T.Rennenberg, A.Hilgenfeld, R.

(2011) Structure 19: 919-929

  • DOI: https://doi.org/10.1016/j.str.2011.03.025
  • Primary Citation Related Structures: 
    3PNR

  • PubMed Abstract: 

    Plasmodium cysteine proteases are essential for host-cell invasion and egress, hemoglobin degradation, and intracellular development of the parasite. The temporal, site-specific regulation of cysteine-protease activity is a prerequisite for survival and propagation of Plasmodium. Recently, a new family of inhibitors of cysteine proteases (ICPs) with homologs in at least eight Plasmodium species has been identified. Here, we report the 2.6 Å X-ray crystal structure of the C-terminal, inhibitory domain of ICP from P. berghei (PbICP-C) in a 1:1 complex with falcipain-2, an important hemoglobinase of Plasmodium. The structure establishes Plasmodium ICP as a member of the I42 class of chagasin-like protease inhibitors but with large insertions and differences in the binding mode relative to other family members. Furthermore, the PbICP-C structure explains why host-cell cathepsin B-like proteases and, most likely, also the protease-like domain of Plasmodium SERA5 (serine-repeat antigen 5) are no targets for ICP.


  • Organizational Affiliation
    • Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, 23538 Lübeck, Germany.

Macromolecule Content 

  • Total Structure Weight: 48.77 kDa 
  • Atom Count: 2,990 
  • Modeled Residue Count: 369 
  • Deposited Residue Count: 427 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Falcipain 2240Plasmodium falciparumMutation(s): 1 
EC: 3.4.22
UniProt
Find proteins for Q8I6U4 (Plasmodium falciparum (isolate 3D7))
Explore Q8I6U4 
Go to UniProtKB:  Q8I6U4
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8I6U4
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
PbICP-C187Plasmodium bergheiMutation(s): 0 
Gene Names: PB000502.02.0

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free:  0.229 (Depositor), 0.217 (DCC) 
  • R-Value Work:  0.181 (Depositor), 0.173 (DCC) 
  • R-Value Observed: 0.183 (Depositor) 
Space Group: P 43
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.15α = 90
b = 71.15β = 90
c = 120.09γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
PHASERphasing
PHENIXrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-07-27
    Type: Initial release
  • Version 1.1: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.2: 2024-11-27
    Changes: Structure summary