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- EMDB-48174: Clostridioides difficile Transferase B Component Trimer in Comple... -

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Basic information

Entry
Database: EMDB / ID: EMD-48174
TitleClostridioides difficile Transferase B Component Trimer in Complex with the A Component
Map dataCDTb trimer-CDTa map.
Sample
  • Complex: Clostridioides difficile Transferase Component B dimer in complex with the A Component
    • Protein or peptide: Adp-ribosyltransferase binding component
    • Protein or peptide: Cdta (Adp-ribosyltransferase enzymatic component)
  • Ligand: CALCIUM ION
KeywordsToxin / Clostridioides / Iota / ADP-ribosyltransferase
Function / homology
Function and homology information


protein homooligomerization / extracellular region
Similarity search - Function
Binary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 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 ...Binary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / 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 / Cdta (Adp-ribosyltransferase enzymatic component)
Similarity search - Component
Biological speciesClostridioides difficile R20291 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.86 Å
AuthorsSheedlo MJ / Mullard RM
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R00AI154672 United States
CitationJournal: PLoS Pathog / Year: 2025
Title: Oligomerization of the Clostridioides difficile transferase B component proceeds through a stepwise mechanism.
Authors: Robin M Mullard / Michael J Sheedlo /
Abstract: Clostridioides difficile is a gram-positive, pathogenic bacterium and is currently the leading cause of hospital-acquired, infectious diarrhea in the United States. During infection, C. difficile ...Clostridioides difficile is a gram-positive, pathogenic bacterium and is currently the leading cause of hospital-acquired, infectious diarrhea in the United States. During infection, C. difficile produces and secretes up to three toxins called Toxin A, Toxin B, and the C. difficile transferase (CDT). While Toxin A and Toxin B are thought to drive the pathology associated with the disease, strains that produce CDT have been linked to increased disease severity, higher rates of infection recurrence, and increased incidence of mortality. A basic understanding of how CDT intoxicates host cells has emerged over the past two decades and includes a framework that relies on the oligomerization of the components that comprise CDT to promote cellular intoxication. Although several key steps of this process have been biochemically described, a clear, molecular description of toxin assembly has not been resolved. We have collected cryogenic electron microscopy (Cryo-EM) data of purified, recombinant CDT. From these data, we have generated several structural snapshots of the toxin, including a series of structures that correspond to intermediates that form during oligomerization. These structures provide insight into the mechanism underlying toxin assembly and highlight a role for structural plasticity during this process. We have also shown that these partially assembled toxins are equally potent in cytotoxicity assays supporting this model in a cellular context. Finally, we show that CDTb oligomers are stabilized by CDTa and assembly is triggered by hydrophobic molecules.
History
DepositionDec 5, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateAug 6, 2025-
Current statusAug 6, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48174.png

Downloads & links

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Map

FileDownload / File: emd_48174.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCDTb trimer-CDTa map.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.86 Å/pix.
x 340 pix.
= 292.4 Å		0.86 Å/pix.
x 340 pix.
= 292.4 Å		0.86 Å/pix.
x 340 pix.
= 292.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.86 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.28200853 - 0.7206923
Average (Standard dev.)0.0018606129 (±0.034396783)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 292.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: CDTb trimer-CDTa half map B.

Fileemd_48174_half_map_1.map
AnnotationCDTb trimer-CDTa half map B.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CDTb trimer-CDTa half map A.

Fileemd_48174_half_map_2.map
AnnotationCDTb trimer-CDTa half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Clostridioides difficile Transferase Component B dimer in complex...

EntireName: Clostridioides difficile Transferase Component B dimer in complex with the A Component
Components
  • Complex: Clostridioides difficile Transferase Component B dimer in complex with the A Component
    • Protein or peptide: Adp-ribosyltransferase binding component
    • Protein or peptide: Cdta (Adp-ribosyltransferase enzymatic component)
  • Ligand: CALCIUM ION

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Supramolecule #1: Clostridioides difficile Transferase Component B dimer in complex...

SupramoleculeName: Clostridioides difficile Transferase Component B dimer in complex with the A Component
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Molecular weightTheoretical: 274 KDa

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Macromolecule #1: Adp-ribosyltransferase binding component

MacromoleculeName: Adp-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Molecular weightTheoretical: 98.916828 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKL LDKDKSDVKS IRWTGRIIPS KDGEYTLSTD RDDVLMQVNT ESTISNTLKV NMKKGKEYKV RIELQDKNLG S IDNLSSPN ...String:
MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKL LDKDKSDVKS IRWTGRIIPS KDGEYTLSTD RDDVLMQVNT ESTISNTLKV NMKKGKEYKV RIELQDKNLG S IDNLSSPN LYWELDGMKK IIPEENLFLR DYSNIEKDDP FIPNNNFFDP KLMSDWEDED LDTDNDNIPD SYERNGYTIK DL IAVKWED SFAEQGYKKY VSNYLESNTA GDPYTDYEKA SGSFDKAIKT EARDPLVAAY PIVGVGMEKL IISTNEHAST DQG KTVSRA TTNSKTESNT AGVSVNVGYQ NGFTANVTTN YSHTTDNSTA VQDSNGESWN TGLSINKGES AYINANVRYY NTGT APMYK VTPTTNLVLD GDTLSTIKAQ ENQIGNNLSP GDTYPKKGLS PLALNTMDQF SSRLIPINYD QLKKLDAGKQ IKLET TQVS GNFGTKNSSG QIVTEGNSWS DYISQIDSIS ASIILDTENE SYERRVTAKN LQDPEDKTPE LTIGEAIEKA FGATKK DGL LYFNDIPIDE SCVELIFDDN TANKIKDSLK TLSDKKIYNV KLERGMNILI KTPTYFTNFD DYNNYPSTWS NVNTTNQ DG LQGSANKLNG ETKIKIPMSE LKPYKRYVFS GYSKDPLTSN SIIVKIKAKE EKTDYLVPEQ GYTKFSYEFE TTEKDSSN I EITLIGSGTT YLDNLSITEL NSTPEILDEP EVKIPTDQEI MDAHKIYFAD LNFNPSTGNT YINGMYFAPT QTNKEALDY IQKYRVEATL QYSGFKDIGT KDKEMRNYLG DPNQPKTNYV NLRSYFTGGE NIMTYKKLRI YAITPDDREL LVLSVD

UniProtKB: Adp-ribosyltransferase binding component

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Macromolecule #2: Cdta (Adp-ribosyltransferase enzymatic component)

MacromoleculeName: Cdta (Adp-ribosyltransferase enzymatic component) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Molecular weightTheoretical: 48.816914 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: YSEKVCNTTY KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRN AISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD E KPTPLLMH ...String:
YSEKVCNTTY KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRN AISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD E KPTPLLMH LKLPRNTGML PYTNTNNVST LIEQGYSIKI DKIVRIVIDG KHYIKAEASV VSSLDFKDDV SKGDSWGKAN YN DWSNKLT PNELADVNDY MRGGYTAINN YLISNGPVNN PNPELDSKIT NIENALKREP IPTNLTVYRR SGPQEFGLTL TSP EYDFNK LENIDAFKSK WEGQALSYPN FISTSIGSVN MSAFAKRKIV LRITIPKGSP GAYLSAIPGY AGEYEVLLNH GSKF KINKI DSYKDGTITK LIVDATLIP

UniProtKB: Cdta (Adp-ribosyltransferase enzymatic component)

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / Number of copies: 9 / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 679889
CTF correctionSoftware - Name: cryoSPARC (ver. v4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.86 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 4436
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT
Output model

PDB-9mdn:
Clostridioides difficile Transferase B Component Trimer in Complex with the A Component

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