6UWI

Crystal structure of the Clostridium difficile translocase CDTb


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure of the cell-binding component of theClostridium difficilebinary toxin reveals a di-heptamer macromolecular assembly.

Xu, X.Godoy-Ruiz, R.Adipietro, K.A.Peralta, C.Ben-Hail, D.Varney, K.M.Cook, M.E.Roth, B.M.Wilder, P.T.Cleveland, T.Grishaev, A.Neu, H.M.Michel, S.L.J.Yu, W.Beckett, D.Rustandi, R.R.Lancaster, C.Loughney, J.W.Kristopeit, A.Christanti, S.Olson, J.W.MacKerell, A.D.Georges, A.D.Pozharski, E.Weber, D.J.

(2020) Proc Natl Acad Sci U S A 117: 1049-1058

  • DOI: https://doi.org/10.1073/pnas.1919490117
  • Primary Citation of Related Structures:  
    6UWI, 6UWO, 6UWR, 6UWT

  • PubMed Abstract: 

    Targeting Clostridium difficile infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent C. difficile strains often have a binary toxin termed the C. difficile toxin, in addition to the enterotoxins TsdA and TsdB. The C. difficile toxin has an enzymatic component, termed CDTa, and a pore-forming or delivery subunit termed CDTb. CDTb was characterized here using a combination of single-particle cryoelectron microscopy, X-ray crystallography, NMR, and other biophysical methods. In the absence of CDTa, 2 di-heptamer structures for activated CDTb (1.0 MDa) were solved at atomic resolution, including a symmetric ( Sym CDTb; 3.14 Å) and an asymmetric form ( Asym CDTb; 2.84 Å). Roles played by 2 receptor-binding domains of activated CDTb were of particular interest since the receptor-binding domain 1 lacks sequence homology to any other known toxin, and the receptor-binding domain 2 is completely absent in other well-studied heptameric toxins (i.e., anthrax). For Asym CDTb, a Ca 2+ binding site was discovered in the first receptor-binding domain that is important for its stability, and the second receptor-binding domain was found to be critical for host cell toxicity and the di-heptamer fold for both forms of activated CDTb. Together, these studies represent a starting point for developing structure-based drug-design strategies to target the most severe strains of C. difficile .


  • Organizational Affiliation

    City University of New York Advanced Science Research Center, City University of New York, New York, NY 10017.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADP-ribosyltransferase binding component667Clostridioides difficileMutation(s): 0 
Gene Names: cdtB
Membrane Entity: Yes 
UniProt
Find proteins for O32739 (Clostridioides difficile)
Explore O32739 
Go to UniProtKB:  O32739
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO32739
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download Ideal Coordinates CCD File 
AB [auth I]
AC [auth f]
AD [auth l]
BB [auth I]
BC [auth e]
AB [auth I],
AC [auth f],
AD [auth l],
BB [auth I],
BC [auth e],
BD [auth l],
CA [auth A],
CB [auth I],
CC [auth e],
CD [auth m],
DA [auth A],
DB [auth J],
DC [auth e],
DD [auth m],
EA [auth A],
EB [auth J],
EC [auth d],
ED [auth m],
FA [auth G],
FB [auth J],
FC [auth d],
FD [auth n],
GA [auth G],
GB [auth K],
GC [auth d],
GD [auth n],
HA [auth G],
HB [auth K],
HC [auth c],
HD [auth n],
IA [auth F],
IB [auth K],
IC [auth c],
JA [auth F],
JB [auth L],
JC [auth c],
KA [auth F],
KB [auth L],
KC [auth b],
LA [auth E],
LB [auth L],
LC [auth b],
MA [auth E],
MB [auth M],
MC [auth b],
NA [auth E],
NB [auth M],
NC [auth h],
OA [auth D],
OB [auth M],
OC [auth h],
PA [auth D],
PB [auth N],
PC [auth h],
QA [auth D],
QB [auth N],
QC [auth i],
RA [auth C],
RB [auth N],
RC [auth i],
SA [auth C],
SB [auth a],
SC [auth i],
TA [auth C],
TB [auth a],
TC [auth j],
UA [auth B],
UB [auth a],
UC [auth j],
VA [auth B],
VB [auth g],
VC [auth j],
WA [auth B],
WB [auth g],
WC [auth k],
XA [auth H],
XB [auth g],
XC [auth k],
YA [auth H],
YB [auth f],
YC [auth k],
ZA [auth H],
ZB [auth f],
ZC [auth l]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.70 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.248 
  • R-Value Observed: 0.250 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 190.485α = 108.742
b = 190.961β = 94.473
c = 192.254γ = 108.031
Software Package:
Software NamePurpose
PHENIXrefinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-01-22
    Type: Initial release
  • Version 1.1: 2024-03-06
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-04-03
    Changes: Refinement description