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- PDB-6uwt: Clostridium difficile binary toxin translocase CDTb tetradecamer ... -

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Basic information

Entry
Database: PDB / ID: 6uwt
TitleClostridium difficile binary toxin translocase CDTb tetradecamer in symmetric conformation
ComponentsADP-ribosyltransferase binding component
KeywordsTOXIN / CDTb / translocase / tetradecamer
Function / homology
Function and homology information


protein homooligomerization / transferase activity / extracellular region / metal ion binding
Similarity search - Function
Protective antigen, heptamerisation domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain ...Protective antigen, heptamerisation domain / Bacterial exotoxin B / Protective antigen, heptamerisation domain / Protective antigen, Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA, domain 3 / Protective antigen, heptamerisation domain superfamily / Clostridial binary toxin B/anthrax toxin PA Ca-binding domain / Clostridial binary toxin B/anthrax toxin PA domain 2 / Clostridial binary toxin B/anthrax toxin PA domain 3 / PA14 domain / PA14 / PA14 domain / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
ADP-ribosyltransferase binding component
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å
AuthorsXu, X. / Pozharski, E. / des Georges, A.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2020
Title: Structure of the cell-binding component of the binary toxin reveals a di-heptamer macromolecular assembly.
Authors: Xingjian Xu / Raquel Godoy-Ruiz / Kaylin A Adipietro / Christopher Peralta / Danya Ben-Hail / Kristen M Varney / Mary E Cook / Braden M Roth / Paul T Wilder / Thomas Cleveland / Alexander ...Authors: Xingjian Xu / Raquel Godoy-Ruiz / Kaylin A Adipietro / Christopher Peralta / Danya Ben-Hail / Kristen M Varney / Mary E Cook / Braden M Roth / Paul T Wilder / Thomas Cleveland / Alexander Grishaev / Heather M Neu / Sarah L J Michel / Wenbo Yu / Dorothy Beckett / Richard R Rustandi / Catherine Lancaster / John W Loughney / Adam Kristopeit / Sianny Christanti / Jessica W Olson / Alexander D MacKerell / Amedee des Georges / Edwin Pozharski / David J Weber /
Abstract: Targeting infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent strains often have a binary toxin termed ...Targeting infection is challenging because treatment options are limited, and high recurrence rates are common. One reason for this is that hypervirulent strains often have a binary toxin termed the toxin, in addition to the enterotoxins TsdA and TsdB. The 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 (CDTb; 3.14 Å) and an asymmetric form (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 CDTb, a Ca 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 .
History
DepositionNov 5, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id

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Structure visualization

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Assembly

Deposited unit
H: ADP-ribosyltransferase binding component
I: ADP-ribosyltransferase binding component
J: ADP-ribosyltransferase binding component
K: ADP-ribosyltransferase binding component
L: ADP-ribosyltransferase binding component
M: ADP-ribosyltransferase binding component
N: ADP-ribosyltransferase binding component
A: ADP-ribosyltransferase binding component
B: ADP-ribosyltransferase binding component
C: ADP-ribosyltransferase binding component
D: ADP-ribosyltransferase binding component
E: ADP-ribosyltransferase binding component
F: ADP-ribosyltransferase binding component
G: ADP-ribosyltransferase binding component
hetero molecules


Theoretical massNumber of molelcules
Total (without water)1,046,62942
Polymers1,045,50714
Non-polymers1,12228
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: SAXS, gel filtration, equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
ADP-ribosyltransferase binding component


Mass: 74679.086 Da / Num. of mol.: 14
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: cdtB / Production host: Escherichia coli (E. coli) / References: UniProt: O32739
#2: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 28 / Source method: obtained synthetically / Formula: Ca
Has ligand of interestN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CDTb tetradecamer / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 1.05 MDa / Experimental value: YES
Source (natural)Organism: Clostridioides difficile (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 56.9 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.17.1_3660refinement
PHENIX1.17.1_3660refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C7 (7 fold cyclic)
3D reconstructionResolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 19944 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 21.6 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.008374060
ELECTRON MICROSCOPYf_angle_d0.8026100534
ELECTRON MICROSCOPYf_chiral_restr0.055211312
ELECTRON MICROSCOPYf_plane_restr0.004613132
ELECTRON MICROSCOPYf_dihedral_angle_d10.35719996

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