6SB5

CryoEM structure of murine perforin-2 ectodomain in a pore form


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.00 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

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

  • DOI: https://doi.org/10.1126/sciadv.aax8286
  • Primary Citation of 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.


  • Organizational Affiliation

    Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK.


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
646Mus 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 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth F]
BA [auth F]
CA [auth G]
DA [auth G]
EA [auth H]
AA [auth F],
BA [auth F],
CA [auth G],
DA [auth G],
EA [auth H],
FA [auth H],
GA [auth I],
HA [auth I],
IA [auth J],
JA [auth J],
KA [auth K],
LA [auth K],
MA [auth L],
NA [auth L],
OA [auth M],
PA [auth M],
Q [auth A],
QA [auth N],
R [auth A],
RA [auth N],
S [auth B],
SA [auth O],
T [auth B],
TA [auth O],
U [auth C],
UA [auth P],
V [auth C],
VA [auth P],
W [auth D],
X [auth D],
Y [auth E],
Z [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: 5.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONRELION

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (MRC, United Kingdom)United KingdomMR/N000331/1

Revision History  (Full details and data files)

  • Version 1.0: 2020-02-05
    Type: Initial release
  • Version 1.1: 2020-02-26
    Changes: Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary