7U1Z | pdb_00007u1z

Crystal structure of the DRBD and CROPs of TcdA

• PDB DOI: https://doi.org/10.2210/pdb7U1Z/pdb

• Classification: TOXIN
• Organism(s): Clostridioides difficile
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-02-22 Released: 2022-03-09 
• Deposition Author(s): Baohua, C., Peng, C., Kay, P., Rongsheng, J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free: 
  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work: 
  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Models: experimental

Literature

Structure and conformational dynamics of Clostridioides difficile toxin A.

Chen, B., Basak, S., Chen, P., Zhang, C., Perry, K., Tian, S., Yu, C., Dong, M., Huang, L., Bowen, M.E., Jin, R.

(2022) Life Sci Alliance 5

• PubMed: 35292538 
• DOI: https://doi.org/10.26508/lsa.202201383
• Primary Citation Related Structures: 
  7U1Z


• PubMed Abstract: 
  

  Clostridioides difficile toxin A and B (TcdA and TcdB) are two major virulence factors responsible for diseases associated with C. difficile infection (CDI). Here, we report the 3.18-Å resolution crystal structure of a TcdA fragment (residues L843-T2481), which advances our understanding of the complete structure of TcdA holotoxin. Our structural analysis, together with complementary single molecule FRET and limited proteolysis studies, reveal that TcdA adopts a dynamic structure and its CROPs domain can sample a spectrum of open and closed conformations in a pH-dependent manner. Furthermore, a small globular subdomain (SGS) and the CROPs protect the pore-forming region of TcdA in the closed state at neutral pH, which could contribute to modulating the pH-dependent pore formation of TcdA. A rationally designed TcdA mutation that trapped the CROPs in the closed conformation showed drastically reduced cytotoxicity. Taken together, these studies shed new lights into the conformational dynamics of TcdA and its roles in TcdA intoxication.

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Organizational Affiliation: 
• Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA.
Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA.
NE-CAT and Department of Chemistry and Chemical Biology, Cornell University, Argonne National Laboratory, Argonne, IL, USA.
Department of Urology, Boston Children's Hospital, Department of Microbiology and Department of Surgery, Harvard Medical School, Boston, MA, USA.
Department of Physiology and Biophysics, Stony Brook University, Stony Brook, NY, USA [e-mail] [e-mail].
Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 375.33 kDa 
• Atom Count: 25,621 
• Modeled Residue Count: 3,232 
• Deposited Residue Count: 3,280 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Toxin A	A [auth B], B [auth A]	1,640	Clostridioides difficile	Mutation(s): 0  Gene Names: tcdA, toxA EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile) Explore P16154  Go to UniProtKB:  P16154

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4 (Subject of Investigation/LOI)	AA [auth A], BA [auth A], C [auth B], CA [auth A], D [auth B], DA [auth A], E [auth B], EA [auth A], F [auth B], FA [auth A], G [auth B], GA [auth A], H [auth B], HA [auth A], I [auth B], IA [auth A], J [auth B], JA [auth A], K [auth B], KA [auth A], L [auth B], LA [auth A], M [auth B], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth A], X [auth A], Y [auth A], Z [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.18 Å
• R-Value Free:  0.254 (Depositor), 0.255 (DCC) 
• R-Value Work:  0.207 (Depositor), 0.208 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 379.507	α = 90
b = 187.641	β = 101.297
c = 95.324	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2022-03-09 
Deposition Author(s): Baohua, C., Peng, C., Kay, P., Rongsheng, J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R01AI125704
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI156092
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	R21AI163178
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30 GM124165

Revision History  

• Version 1.0: 2022-03-09
  Type: Initial release
  
• Version 1.1: 2022-03-23
  Changes: Database references
• Version 1.2: 2022-03-30
  Changes: Database references
• Version 1.3: 2023-10-18
  Changes: Data collection, Refinement description