7S0Z

Structures of TcdB in complex with R-Ras


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Models: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis for selective modification of Rho and Ras GTPases by Clostridioides difficile toxin B.

Liu, Z.Zhang, S.Chen, P.Tian, S.Zeng, J.Perry, K.Dong, M.Jin, R.

(2021) Sci Adv 7: eabi4582-eabi4582

  • DOI: https://doi.org/10.1126/sciadv.abi4582
  • Primary Citation of Related Structures:  
    7S0Y, 7S0Z

  • PubMed Abstract: 

    Toxin B (TcdB) is a primary cause of Clostridioides difficile infection (CDI). This toxin acts by glucosylating small GTPases in the Rho/Ras families, but the structural basis for TcdB recognition and selectivity of specific GTPase substrates remain unsolved. Here, we report the cocrystal structures of the glucosyltransferase domain (GTD) of two distinct TcdB variants in complex with human Cdc42 and R-Ras, respectively. These structures reveal a common structural mechanism by which TcdB recognizes Rho and R-Ras. Furthermore, we find selective clustering of adaptive residue changes in GTDs that determine their substrate preferences, which helps partition all known TcdB variants into two groups that display distinct specificities toward Rho or R-Ras. Mutations that selectively disrupt GTPases binding reduce the glucosyltransferase activity of the GTD and the toxicity of TcdB holotoxin. These findings establish the structural basis for TcdB recognition of small GTPases and reveal strategies for therapeutic interventions for CDI.


  • Organizational Affiliation

    Department of Physiology and Biophysics, University of California, Irvine, Irvine, CA 92697, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Toxin BA [auth B],
B [auth A]
541Clostridioides difficileMutation(s): 0 
Gene Names: tcdBSAMEA708418_03270
EC: 2.4.1 (PDB Primary Data), 3.4.22 (UniProt)
UniProt
Find proteins for Q9EXR0 (Clostridioides difficile)
Explore Q9EXR0 
Go to UniProtKB:  Q9EXR0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9EXR0
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ras-related protein R-Ras
C, D
179Homo sapiensMutation(s): 0 
Gene Names: RRAS
EC: 3.6.5
UniProt & NIH Common Fund Data Resources
Find proteins for P10301 (Homo sapiens)
Explore P10301 
Go to UniProtKB:  P10301
PHAROS:  P10301
GTEx:  ENSG00000126458 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10301
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 9 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download Ideal Coordinates CCD File 
BB [auth D],
ZA [auth C]
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
UDP
Query on UDP

Download Ideal Coordinates CCD File 
E [auth B],
W [auth A]
URIDINE-5'-DIPHOSPHATE
C9 H14 N2 O12 P2
XCCTYIAWTASOJW-XVFCMESISA-N
GLC
Query on GLC

Download Ideal Coordinates CCD File 
SA [auth A],
T [auth B]
alpha-D-glucopyranose
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
P [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth A]
CA [auth A]
G [auth B]
H [auth B]
J [auth B]
AA [auth A],
CA [auth A],
G [auth B],
H [auth B],
J [auth B],
M [auth B],
O [auth B],
U [auth B],
UA [auth A],
VA [auth C],
WA [auth C],
Y [auth A],
Z [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT
Query on ACT

Download Ideal Coordinates CCD File 
AB [auth D]
BA [auth A]
DA [auth A]
FA [auth A]
GA [auth A]
AB [auth D],
BA [auth A],
DA [auth A],
FA [auth A],
GA [auth A],
IA [auth A],
JA [auth A],
K [auth B],
KA [auth A],
L [auth B],
LA [auth A],
N [auth B],
RA [auth A],
V [auth B],
YA [auth C]
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN
Query on MN

Download Ideal Coordinates CCD File 
NA [auth A],
Q [auth B]
MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
CB [auth D],
OA [auth A],
PA [auth A],
QA [auth A],
TA [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NH4
Query on NH4

Download Ideal Coordinates CCD File 
EA [auth A]
F [auth B]
HA [auth A]
I [auth B]
MA [auth A]
EA [auth A],
F [auth B],
HA [auth A],
I [auth B],
MA [auth A],
R [auth B],
S [auth B],
X [auth A],
XA [auth C]
AMMONIUM ION
H4 N
QGZKDVFQNNGYKY-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.34 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 76.308α = 90
b = 112.112β = 95.89
c = 101.571γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHENIXphasing

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 General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-08
    Type: Initial release
  • Version 1.1: 2022-03-23
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description