7KXR | pdb_00007kxr

Protective antigen pore translocating lethal factor N-terminal domain


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 7KXR

This is version 1.1 of the entry. See complete history

Literature

Anthrax toxin translocation complex reveals insight into the lethal factor unfolding and refolding mechanism.

Machen, A.J.Fisher, M.T.Freudenthal, B.D.

(2021) Sci Rep 11: 13038-13038

  • DOI: https://doi.org/10.1038/s41598-021-91596-3
  • Primary Citation Related Structures: 
    7KXR

  • PubMed Abstract: 

    Translocation is essential to the anthrax toxin mechanism. Protective antigen (PA), the binding component of this AB toxin, forms an oligomeric pore that translocates lethal factor (LF) or edema factor, the active components of the toxin, into the cell. Structural details of the translocation process have remained elusive despite their biological importance. To overcome the technical challenges of studying translocation intermediates, we developed a method to immobilize, transition, and stabilize anthrax toxin to mimic important physiological steps in the intoxication process. Here, we report a cryoEM snapshot of PA pore translocating the N-terminal domain of LF (LF N ). The resulting 3.3 Å structure of the complex shows density of partially unfolded LF N near the canonical PA pore binding site. Interestingly, we also observe density consistent with an α helix emerging from the 100 Å β barrel channel suggesting LF secondary structural elements begin to refold in the pore channel. We conclude the anthrax toxin β barrel aids in efficient folding of its enzymatic payload prior to channel exit. Our hypothesized refolding mechanism has broader implications for pore length of other protein translocating toxins.


  • Organizational Affiliation
    • Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, USA.

Macromolecule Content 

  • Total Structure Weight: 472.21 kDa 
  • Atom Count: 32,826 
  • Modeled Residue Count: 4,154 
  • Deposited Residue Count: 4,197 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Lethal factorA [auth L]263Bacillus anthracisMutation(s): 1 
Gene Names: lefpXO1-107BXA0172GBAA_pXO1_0172
EC: 3.4.24.83
Membrane Entity: Yes 
UniProt
Find proteins for P15917 (Bacillus anthracis)
Explore P15917 
Go to UniProtKB:  P15917
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP15917
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Protective antigen562Bacillus anthracisMutation(s): 0 
Gene Names: pagApagpXO1-110BXA0164GBAA_pXO1_0164
Membrane Entity: Yes 
UniProt
Find proteins for P13423 (Bacillus anthracis)
Explore P13423 
Go to UniProtKB:  P13423
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13423
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA

Query on CA



Download:Ideal Coordinates CCD File
I [auth A]
J [auth A]
K [auth B]
L [auth B]
M [auth C]
I [auth A],
J [auth A],
K [auth B],
L [auth B],
M [auth C],
N [auth C],
O [auth D],
P [auth D],
Q [auth E],
R [auth E],
S [auth F],
T [auth F],
U [auth G],
V [auth G]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.30 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR03-AI142361

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references