4Y1S | pdb_00004y1s

Structural basis for Ca2+-mediated interaction of the perforin C2 domain with lipid membranes

• PDB DOI: https://doi.org/10.2210/pdb4Y1S/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Mus musculus
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-02-09 Released: 2015-09-02 
• Deposition Author(s): Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free: 
  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work: 
  0.166 (Depositor) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Structural Basis for Ca2+-mediated Interaction of the Perforin C2 Domain with Lipid Membranes.

Yagi, H., Conroy, P.J., Leung, E.W., Law, R.H., Trapani, J.A., Voskoboinik, I., Whisstock, J.C., Norton, R.S.

(2015) J Biological Chem 290: 25213-25226

• PubMed: 26306037 
• DOI: https://doi.org/10.1074/jbc.M115.668384
• Primary Citation Related Structures: 
  4Y1S, 4Y1T


• PubMed Abstract: 
  

  Natural killer cells and cytotoxic T-lymphocytes deploy perforin and granzymes to kill infected host cells. Perforin, secreted by immune cells, binds target membranes to form pores that deliver pro-apoptotic granzymes into the target cell. A crucial first step in this process is interaction of its C2 domain with target cell membranes, which is a calcium-dependent event. Some aspects of this process are understood, but many molecular details remain unclear. To address this, we investigated the mechanism of Ca(2+) and lipid binding to the C2 domain by NMR spectroscopy and x-ray crystallography. Calcium titrations, together with dodecylphosphocholine micelle experiments, confirmed that multiple Ca(2+) ions bind within the calcium-binding regions, activating perforin with respect to membrane binding. We have also determined the affinities of several of these binding sites and have shown that this interaction causes a significant structural rearrangement in CBR1. Thus, it is proposed that Ca(2+) binding at the weakest affinity site triggers changes in the C2 domain that facilitate its interaction with lipid membranes.

---

Organizational Affiliation: 
• From the Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052.
the Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800.
the Cancer Immunology Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, and the Departments of Microbiology and Immunology and.
the Cancer Immunology Program, Peter MacCallum Cancer Centre, East Melbourne, Victoria 3002, and the Departments of Microbiology and Immunology and Genetics and Pathology, University of Melbourne, Parkville, Victoria 3052, Australia.
the Department of Biochemistry and Molecular Biology and ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Clayton, Victoria 3800, [e-mail].
From the Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 16.52 kDa 
• Atom Count: 1,120 
• Modeled Residue Count: 122 
• Deposited Residue Count: 149 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Perforin-1	A	149	Mus musculus	Mutation(s): 4  Gene Names: Prf1, Pfp
UniProt & NIH Common Fund Data Resources
Find proteins for P10820 (Mus musculus) Explore P10820  Go to UniProtKB:  P10820
IMPC:  MGI:97551

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.61 Å
• R-Value Free:  0.185 (Depositor), 0.195 (DCC) 
• R-Value Work:  0.166 (Depositor) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 37.7	α = 90
b = 43.211	β = 90
c = 68.077	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Blu-Ice	data collection
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-02 
Deposition Author(s): Conroy, P.J., Yagi, H., Whisstock, J.C., Norton, R.S.

Revision History  

• Version 1.0: 2015-09-02
  Type: Initial release
  
• Version 1.1: 2015-09-09
  Changes: Database references
• Version 1.2: 2015-10-28
  Changes: Database references
• Version 1.3: 2017-12-13
  Changes: Data collection, Database references, Derived calculations, Source and taxonomy
• Version 1.4: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.5: 2024-11-06
  Changes: Structure summary