5UG7 | pdb_00005ug7

Calcium bound Perforin C2 Domain - T431D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work: 
    0.211 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.5 of the entry. See complete history

Literature

Perforin proteostasis is regulated through its C2 domain: supra-physiological cell death mediated by T431D-perforin.

Brennan, A.J.Law, R.H.P.Conroy, P.J.Noori, T.Lukoyanova, N.Saibil, H.Yagita, H.Ciccone, A.Verschoor, S.Whisstock, J.C.Trapani, J.A.Voskoboinik, I.

(2018) Cell Death Differ 25: 1517-1529

  • DOI: https://doi.org/10.1038/s41418-018-0057-z
  • Primary Citation Related Structures: 
    5UG6, 5UG7

  • PubMed Abstract: 

    The pore forming, Ca 2+ -dependent protein, perforin, is essential for the function of cytotoxic lymphocytes, which are at the frontline of immune defence against pathogens and cancer. Perforin is a glycoprotein stored in the secretory granules prior to release into the immune synapse. Congenital perforin deficiency causes fatal immune dysregulation, and is associated with various haematological malignancies. At least 50% of pathological missense mutations in perforin result in protein misfolding and retention in the endoplasmic reticulum. However, the regulation of perforin proteostasis remains unexplored. Using a variety of biochemical assays that assess protein stability and acquisition of complex glycosylation, we demonstrated that the binding of Ca 2+ to the C2 domain stabilises perforin and regulates its export from the endoplasmic reticulum to the secretory granules. As perforin is a thermo-labile protein, we hypothesised that by altering its C2 domain it may be possible to improve protein stability. On the basis of the X-ray crystal structure of the perforin C2 domain, we designed a mutation (T431D) in the Ca 2+ binding loop. Mutant perforin displayed markedly enhanced thermal stability and lytic function, despite its trafficking from the endoplasmic reticulum remaining unchanged. Furthermore, by introducing the T431D mutation into A90V perforin, a pathogenic mutation, which results in protein misfolding, we corrected the A90V folding defect and completely restored perforin's cytotoxic function. These results revealed an unexpected role for the Ca 2+ -dependent C2 domain in maintaining perforin proteostasis and demonstrated the possibility of designing perforin with supra-physiological cytotoxic function through stabilisation of the C2 domain.


  • Organizational Affiliation
    • Killer Cell Biology Laboratory, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia. amelia.brennan@petermac.org.

Macromolecule Content 

  • Total Structure Weight: 16.61 kDa 
  • Atom Count: 1,072 
  • Modeled Residue Count: 126 
  • Deposited Residue Count: 149 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Perforin-1149Mus musculusMutation(s): 5 
Gene Names: Prf1Pfp
UniProt & NIH Common Fund Data Resources
Find proteins for P10820 (Mus musculus)
Explore P10820 
Go to UniProtKB:  P10820
IMPC:  MGI:97551
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10820
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.233 (Depositor), 0.233 (DCC) 
  • R-Value Work:  0.211 (Depositor), 0.202 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.996α = 90
b = 31.312β = 101.35
c = 86.364γ = 90
Software Package:
Software NamePurpose
Aimlessdata scaling
BUSTERrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-02-07
    Type: Initial release
  • Version 1.1: 2018-02-21
    Changes: Database references
  • Version 1.2: 2018-04-18
    Changes: Data collection
  • Version 1.3: 2018-09-12
    Changes: Data collection, Database references
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-10-09
    Changes: Structure summary