6SB1 | pdb_00006sb1

Crystal structure of murine perforin-2 P2 domain crystal form 1

• PDB DOI: https://doi.org/10.2210/pdb6SB1/pdb

• Classification: TOXIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 
• Membrane Protein: Yes  OPM


• Deposited: 2019-07-18 Released: 2020-02-05 
• Deposition Author(s): Ni, T., Ginger, L., Gilbert, R.J.C.
• Funding Organization(s): Medical Research Council (United Kingdom)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free: 
  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.212 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Literature

Structure and mechanism of bactericidal mammalian perforin-2, an ancient agent of innate immunity.

Ni, T., Jiao, F., Yu, X., Aden, S., Ginger, L., Williams, S.I., Bai, F., Prazak, V., Karia, D., Stansfeld, P., Zhang, P., Munson, G., Anderluh, G., Scheuring, S., Gilbert, R.J.C.

(2020) Sci Adv 6: eaax8286-eaax8286

• PubMed: 32064340 
• DOI: https://doi.org/10.1126/sciadv.aax8286
• Primary Citation Related Structures: 
  6SB1, 6SB3, 6SB4, 6SB5


• PubMed Abstract: 
  

  Perforin-2 (MPEG1) is thought to enable the killing of invading microbes engulfed by macrophages and other phagocytes, forming pores in their membranes. Loss of perforin-2 renders individual phagocytes and whole organisms significantly more susceptible to bacterial pathogens. Here, we reveal the mechanism of perforin-2 activation and activity using atomic structures of pre-pore and pore assemblies, high-speed atomic force microscopy, and functional assays. Perforin-2 forms a pre-pore assembly in which its pore-forming domain points in the opposite direction to its membrane-targeting domain. Acidification then triggers pore formation, via a 180° conformational change. This novel and unexpected mechanism prevents premature bactericidal attack and may have played a key role in the evolution of all perforin family proteins.

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Organizational Affiliation: 
• Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.
Department of Anesthesiology, Weill Cornell Medical College, 1300 York Ave., New York, NY 10065, USA.
Calleva Research Centre for Evolution and Human Sciences, Magdalen College, University of Oxford, Oxford OX1 4AU, UK.
Department of Molecular Biology and Nanobiotechnology, National Institute of Chemistry, Hajdrihova 19, 1000 Ljubljana, Slovenia.
Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.
Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
Department of Physiology and Biophysics, Weill Cornell Medical College, 1300 York Ave., New York, NY 10065, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 64.9 kDa 
• Atom Count: 3,098 
• Modeled Residue Count: 392 
• Deposited Residue Count: 590 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Macrophage-expressed gene 1 protein	A, B	295	Mus musculus	Mutation(s): 0  Gene Names: Mpeg1 Membrane Entity: Yes
UniProt
Find proteins for A1L314 (Mus musculus) Explore A1L314  Go to UniProtKB:  A1L314

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	C [auth A], D [auth A], F [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.05 Å
• R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.212 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.53	α = 90
b = 31.27	β = 91.42
c = 103.65	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	data scaling
PHENIX	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-02-05 
Deposition Author(s): Ni, T., Ginger, L., Gilbert, R.J.C.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/N000331/1

Revision History  

• Version 1.0: 2020-02-05
  Type: Initial release
  
• Version 1.1: 2020-02-26
  Changes: Database references
• Version 1.2: 2024-11-06
  Changes: Data collection, Database references, Refinement description, Structure summary