8SFG | pdb_00008sfg

Crystal Structure of the Open Unbound Catalytically Inactive Makes Caterpillars Floppy-like (MCF) Effector from Vibrio vulnificus CMCP6


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 
    0.230 (Depositor), 0.219 (DCC) 
  • R-Value Work: 
    0.189 (Depositor) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 8SFG

This is version 1.2 of the entry. See complete history

Literature

Vibrio MARTX toxin processing and degradation of cellular Rab GTPases by the cytotoxic effector Makes Caterpillars Floppy.

Herrera, A.Packer, M.M.Rosas-Lemus, M.Minasov, G.Chen, J.Brumell, J.H.Satchell, K.J.F.

(2024) Proc Natl Acad Sci U S A 121: e2316143121-e2316143121

  • DOI: https://doi.org/10.1073/pnas.2316143121
  • Primary Citation Related Structures: 
    8SFG

  • PubMed Abstract: 

    Vibrio vulnificus causes life-threatening wound and gastrointestinal infections, mediated primarily by the production of a Multifunctional-Autoprocessing Repeats-In-Toxin (MARTX) toxin. The most commonly present MARTX effector domain, the Makes Caterpillars Floppy-like (MCF) toxin, is a cysteine protease stimulated by host adenosine diphosphate (ADP) ribosylation factors (ARFs) to autoprocess. Here, we show processed MCF then binds and cleaves host Ra s-related proteins in b rain (Rab) guanosine triphosphatases within their C-terminal tails resulting in Rab degradation. We demonstrate MCF binds Rabs at the same interface occupied by ARFs. Moreover, we show MCF preferentially binds to ARF1 prior to autoprocessing and is active to cleave Rabs only subsequent to autoprocessing. We then use structure prediction algorithms to demonstrate that structural composition, rather than sequence, determines Rab target specificity. We further determine a crystal structure of aMCF as a swapped dimer, revealing an alternative conformation we suggest represents the open, activated state of MCF with reorganized active site residues. The cleavage of Rabs results in Rab1B dispersal within cells and loss of Rab1B density in the intestinal tissue of infected mice. Collectively, our work describes an extracellular bacterial mechanism whereby MCF is activated by ARFs and subsequently induces the degradation of another small host guanosine triphosphatase (GTPase), Rabs, to drive organelle damage, cell death, and promote pathogenesis of these rapidly fatal infections.


  • Organizational Affiliation
    • Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611.

Macromolecule Content 

  • Total Structure Weight: 163.16 kDa 
  • Atom Count: 10,360 
  • Modeled Residue Count: 1,313 
  • Deposited Residue Count: 1,460 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Autotransporter adhesin
A, B, C, D
365Vibrio vulnificus CMCP6Mutation(s): 1 
Gene Names: VV2_0479
UniProt
Find proteins for A0A3Q0KY79 (Vibrio vulnificus (strain CMCP6))
Explore A0A3Q0KY79 
Go to UniProtKB:  A0A3Q0KY79
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A3Q0KY79
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
HA [auth D],
I [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth B],
Y [auth C],
Z [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CL

Query on CL



Download:Ideal Coordinates CCD File
CA [auth C]
DA [auth C]
EA [auth C]
FA [auth C]
GA [auth C]
CA [auth C],
DA [auth C],
EA [auth C],
FA [auth C],
GA [auth C],
J [auth A],
K [auth A],
L [auth A],
LA [auth D],
M [auth A],
MA [auth D],
N [auth A],
NA [auth D],
O [auth A],
OA [auth D],
P [auth A],
PA [auth D],
Q [auth A],
QA [auth D],
RA [auth D],
W [auth B],
X [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A, B, C, D
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free:  0.230 (Depositor), 0.219 (DCC) 
  • R-Value Work:  0.189 (Depositor) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.381α = 90
b = 160.661β = 101.28
c = 71.793γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States75N93022C00035

Revision History  (Full details and data files)

  • Version 1.0: 2024-06-05
    Type: Initial release
  • Version 1.1: 2024-10-23
    Changes: Structure summary
  • Version 1.2: 2025-09-24
    Changes: Database references