8P50

Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structure and activation mechanism of the Makes caterpillars floppy 1 toxin.

Belyy, A.Heilen, P.Hagel, P.Hofnagel, O.Raunser, S.

(2023) Nat Commun 14: 8226-8226

  • DOI: https://doi.org/10.1038/s41467-023-44069-2
  • Primary Citation of Related Structures:  
    8P50, 8P51, 8P52

  • PubMed Abstract: 

    The bacterial Makes caterpillars floppy 1 (Mcf1) toxin promotes apoptosis in insects, leading to loss of body turgor and death. The molecular mechanism underlying Mcf1 intoxication is poorly understood. Here, we present the cryo-EM structure of Mcf1 from Photorhabdus luminescens, revealing a seahorse-like shape with a head and tail. While the three head domains contain two effectors, as well as an activator-binding domain (ABD) and an autoprotease, the tail consists of two putative translocation and three putative receptor-binding domains. Rearrangement of the tail moves the C-terminus away from the ABD and allows binding of the host cell ADP-ribosylation factor 3, inducing conformational changes that position the cleavage site closer to the protease. This distinct activation mechanism that is based on a hook-loop interaction results in three autocleavage reactions and the release of two toxic effectors. Unexpectedly, the BH3-like domain containing ABD is not an active effector. Our findings allow us to understand key steps of Mcf1 intoxication at the molecular level.


  • Organizational Affiliation

    Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Otto-Hahn-Str. 11, 44227, Dortmund, Germany.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin protein2,934Photorhabdus luminescensMutation(s): 1 
Gene Names: mcf
UniProt
Find proteins for Q8KT65 (Photorhabdus luminescens)
Explore Q8KT65 
Go to UniProtKB:  Q8KT65
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8KT65
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosylation factor 3184Homo sapiensMutation(s): 1 
Gene Names: ARF3
UniProt & NIH Common Fund Data Resources
Find proteins for P61204 (Homo sapiens)
Explore P61204 
Go to UniProtKB:  P61204
PHAROS:  P61204
GTEx:  ENSG00000134287 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61204
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.04 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Max Planck SocietyGermany--

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-01
    Type: Initial release
  • Version 1.1: 2023-12-27
    Changes: Database references