7U1Z

Crystal structure of the DRBD and CROPs of TcdA

  • 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)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.18 Å
  • R-Value Free: 0.254 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history


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

  • DOI: https://doi.org/10.26508/lsa.202201383
  • Primary Citation of 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.


  • Organizational Affiliation

    Department of Physiology and Biophysics, School of Medicine, University of California, Irvine, Irvine, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin AA [auth B],
B [auth A]
1,640Clostridioides difficileMutation(s): 0 
Gene Names: tcdAtoxA
EC: 3.4.22
UniProt
Find proteins for P16154 (Clostridioides difficile)
Explore P16154 
Go to UniProtKB:  P16154
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16154
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4 (Subject of Investigation/LOI)
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A]
BA [auth A]
C [auth B]
CA [auth A]
D [auth B]
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 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 379.507α = 90
b = 187.641β = 101.297
c = 95.324γ = 90
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
PHENIXphasing
PHENIXrefinement

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR01AI125704
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI156092
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21AI163178
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP30 GM124165

Revision History  (Full details and data files)

  • 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