6U2J

EM structure of MPEG-1 (L425K, alpha conformation) soluble pre-pore complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The cryo-EM structure of the acid activatable pore-forming immune effector Macrophage-expressed gene 1.

Pang, S.S.Bayly-Jones, C.Radjainia, M.Spicer, B.A.Law, R.H.P.Hodel, A.W.Parsons, E.S.Ekkel, S.M.Conroy, P.J.Ramm, G.Venugopal, H.Bird, P.I.Hoogenboom, B.W.Voskoboinik, I.Gambin, Y.Sierecki, E.Dunstone, M.A.Whisstock, J.C.

(2019) Nat Commun 10: 4288-4288

  • DOI: 10.1038/s41467-019-12279-2
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, however, its mode of action remains unknown. We use cry ...

    Macrophage-expressed gene 1 (MPEG1/Perforin-2) is a perforin-like protein that functions within the phagolysosome to damage engulfed microbes. MPEG1 is thought to form pores in target membranes, however, its mode of action remains unknown. We use cryo-Electron Microscopy (cryo-EM) to determine the 2.4 Å structure of a hexadecameric assembly of MPEG1 that displays the expected features of a soluble prepore complex. We further discover that MPEG1 prepore-like assemblies can be induced to perforate membranes through acidification, such as would occur within maturing phagolysosomes. We next solve the 3.6 Å cryo-EM structure of MPEG1 in complex with liposomes. These data reveal that a multi-vesicular body of 12 kDa (MVB12)-associated β-prism (MABP) domain binds membranes such that the pore-forming machinery of MPEG1 is oriented away from the bound membrane. This unexpected mechanism of membrane interaction suggests that MPEG1 remains bound to the phagolysosome membrane while simultaneously forming pores in engulfed bacterial targets.


    Organizational Affiliation

    Department of Genetics, The University of Melbourne, Parkville, VIC, 3010, Australia.,Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia.,London Centre for Nanotechnology, University College London, London, WC1H 0AH, UK.,Institute of Structural and Molecular Biology, University College London, London, WC1E 6BT, UK.,EMBL Australia, Single Molecule Node, University of New South Wales, Sydney, 2052, Australia.,Thermo Fischer Scientific, Achtseweg Noord 5, Building 5651 GG, Eindhoven, The Netherlands.,Department of Physics and Astronomy, University College London, London, WC1E 6BT, UK.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia.,Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia. Michelle.Dunstone@monash.edu.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia. Michelle.Dunstone@monash.edu.,ARC Centre of Excellence in Advanced Molecular Imaging, Monash University, Melbourne, VIC, 3800, Australia. James.Whisstock@monash.edu.,EMBL Australia, Monash University, Melbourne, VIC, 3800, Australia. James.Whisstock@monash.edu.,Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology, Monash University, Melbourne, VIC, 3800, Australia. James.Whisstock@monash.edu.,Cancer Immunology Program, Peter MacCallum Cancer Centre, Melbourne, VIC, 3000, Australia.,ACRF Department of Cancer Biology and Therapeutics, John Curtin School of Medical Research, Australian National University, Canberra, ACT, 2601, Australia. James.Whisstock@monash.edu.,School of Medical Science, University of New South Wales, Randwick, NSW, 2052, Australia.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Macrophage-expressed gene 1 protein
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
642Homo sapiensMutation(s): 1 
Gene Names: MPEG1
Find proteins for Q2M385 (Homo sapiens)
Go to Gene View: MPEG1
Go to UniProtKB:  Q2M385
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.37 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Australian Research Council (ARC)Australia--

Revision History 

  • Version 1.0: 2019-09-25
    Type: Initial release
  • Version 1.1: 2019-10-02
    Type: Data collection, Database references
  • Version 1.2: 2020-01-15
    Type: Author supporting evidence