8A1D

Structure of murine perforin-2 (Mpeg1) pore in ring form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 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

Cryo-EM structures of perforin-2 in isolation and assembled on a membrane suggest a mechanism for pore formation.

Yu, X.Ni, T.Munson, G.Zhang, P.Gilbert, R.J.C.

(2022) EMBO J 41: e111857-e111857

  • DOI: https://doi.org/10.15252/embj.2022111857
  • Primary Citation of Related Structures:  
    8A1D, 8A1S

  • PubMed Abstract: 

    Perforin-2 (PFN2, MPEG1) is a key pore-forming protein in mammalian innate immunity restricting intracellular bacteria proliferation. It forms a membrane-bound pre-pore complex that converts to a pore-forming structure upon acidification; but its mechanism of conformational transition has been debated. Here we used cryo-electron microscopy, tomography and subtomogram averaging to determine structures of PFN2 in pre-pore and pore conformations in isolation and bound to liposomes. In isolation and upon acidification, the pre-assembled complete pre-pore rings convert to pores in both flat ring and twisted conformations. On membranes, in situ assembled PFN2 pre-pores display various degrees of completeness; whereas PFN2 pores are mainly incomplete arc structures that follow the same subunit packing arrangements as found in isolation. Both assemblies on membranes use their P2 β-hairpin for binding to the lipid membrane surface. Overall, these structural snapshots suggest a molecular mechanism for PFN2 pre-pore to pore transition on a targeted membrane, potentially using the twisted pore as an intermediate or alternative state to the flat conformation, with the capacity to cause bilayer distortion during membrane insertion.


  • Organizational Affiliation

    Department of Microbiology and Immunology, University of Miami Miller School of Medicine, Miami, FL, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Macrophage-expressed gene 1 protein
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P
648Mus musculusMutation(s): 0 
Gene Names: Mpeg1
Membrane Entity: Yes 
UniProt
Find proteins for A1L314 (Mus musculus)
Explore A1L314 
Go to UniProtKB:  A1L314
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA1L314
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MA4 (Subject of Investigation/LOI)
Query on MA4

Download Ideal Coordinates CCD File 
BA [auth F]
DA [auth G]
FA [auth H]
HA [auth I]
JA [auth J]
BA [auth F],
DA [auth G],
FA [auth H],
HA [auth I],
JA [auth J],
LA [auth K],
NA [auth L],
PA [auth M],
R [auth A],
RA [auth N],
T [auth B],
TA [auth O],
V [auth C],
VA [auth P],
X [auth D],
Z [auth E]
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
NAG (Subject of Investigation/LOI)
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth F]
CA [auth G]
EA [auth H]
GA [auth I]
IA [auth J]
AA [auth F],
CA [auth G],
EA [auth H],
GA [auth I],
IA [auth J],
KA [auth K],
MA [auth L],
OA [auth M],
Q [auth A],
QA [auth N],
S [auth B],
SA [auth O],
U [auth C],
UA [auth P],
W [auth D],
Y [auth E]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom--

Revision History  (Full details and data files)

  • Version 1.0: 2022-07-20
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references
  • Version 1.2: 2022-12-14
    Changes: Database references