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- EMDB-20926: Clostridium difficile binary toxin translocase CDTb in asymmetric... -

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Basic information

Entry
Database: EMDB / ID: EMD-20926
TitleClostridium difficile binary toxin translocase CDTb in asymmetric tetradecamer conformation
Map datatoxin translocase
Sample
  • Complex: Tetradecamer of CDTb
    • Protein or peptide: ADP-ribosyltransferase binding component
  • Ligand: CALCIUM ION
KeywordsTranslocase / binary toxin / TOXIN
Function / homology
Function and homology information


protein homooligomerization / transferase activity / extracellular region / metal ion binding
Similarity search - Function
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
Similarity search - Domain/homology
ADP-ribosyltransferase binding component
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsXu X / Pozharski E
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, 2019-
Header (metadata) releaseDec 4, 2019-
Map releaseJan 22, 2020-
UpdateMar 6, 2024-
Current statusMar 6, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6uwr
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20926.png

Downloads & links

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Map

FileDownload / File: emd_20926.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationtoxin translocase
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å		1.06 Å/pix.
x 400 pix.
= 424. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.10705607 - 0.17696652
Average (Standard dev.)-0.00003222719 (±0.0066782692)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 423.99997 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.061.061.06
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z424.000424.000424.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.1070.177-0.000

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Supplemental data

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Sample components

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Entire : Tetradecamer of CDTb

EntireName: Tetradecamer of CDTb
Components
  • Complex: Tetradecamer of CDTb
    • Protein or peptide: ADP-ribosyltransferase binding component
  • Ligand: CALCIUM ION

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Supramolecule #1: Tetradecamer of CDTb

SupramoleculeName: Tetradecamer of CDTb / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 1.05 MDa

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Macromolecule #1: ADP-ribosyltransferase binding component

MacromoleculeName: ADP-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Number of copies: 14 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 74.679086 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: LMSDWEDEDL DTDNDNIPDS YERNGYTIKD LIAVKWEDSF AEQGYKKYVS NYLESNTAGD PYTDYEKASG SFDKAIKTEA RDPLVAAYP IVGVGMEKLI ISTNEHASTD QGKTVSRATT NSKTESNTAG VSVNVGYQNG FTANVTTNYS HTTDNSTAVQ D SNGESWNT ...String:
LMSDWEDEDL DTDNDNIPDS YERNGYTIKD LIAVKWEDSF AEQGYKKYVS NYLESNTAGD PYTDYEKASG SFDKAIKTEA RDPLVAAYP IVGVGMEKLI ISTNEHASTD QGKTVSRATT NSKTESNTAG VSVNVGYQNG FTANVTTNYS HTTDNSTAVQ D SNGESWNT GLSINKGESA YINANVRYYN TGTAPMYKVT PTTNLVLDGD TLSTIKAQEN QIGNNLSPGD TYPKKGLSPL AL NTMDQFS SRLIPINYDQ LKKLDAGKQI KLETTQVSGN FGTKNSSGQI VTEGNSWSDY ISQIDSISAS IILDTENESY ERR VTAKNL QDPEDKTPEL TIGEAIEKAF GATKKDGLLY FNDIPIDESC VELIFDDNTA NKIKDSLKTL SDKKIYNVKL ERGM NILIK TPTYFTNFDD YNNYPSTWSN VNTTNQDGLQ GSANKLNGET KIKIPMSELK PYKRYVFSGY SKDPLTSNSI IVKIK AKEE KTDYLVPEQG YTKFSYEFET TEKDSSNIEI TLIGSGTTYL DNLSITELNS TPEILDEPEV KIPTDQEIMD AHKIYF ADL NFNPSTGNTY INGMYFAPTQ TNKEALDYIQ KYRVEATLQY SGFKDIGTKD KEMRNYLGDP NQPKTNYVNL RSYFTGG EN IMTYKKLRIY AITPDDRELL VLSVD

UniProtKB: ADP-ribosyltransferase binding component

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Macromolecule #2: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 2 / Number of copies: 42 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 56.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 11122
Initial angle assignmentType: NOT APPLICABLE
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: BACKBONE TRACE
Output model

PDB-6uwr:
Clostridium difficile binary toxin translocase CDTb in asymmetric tetradecamer conformation

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