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- EMDB-48170: Low Resolution Cryo-EM Map of the Clostridioides difficile Transf... -

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Basic information

Entry
Database: EMDB / ID: EMD-48170
TitleLow Resolution Cryo-EM Map of the Clostridioides difficile Transferase Component B Monomer
Map data
Sample
  • Complex: Clostridioides difficile Transferase Component B
    • Protein or peptide: Adp-ribosyltransferase binding component
KeywordsToxin / Clostridioides / Iota / ADP-ribosyltransferase
Biological speciesClostridioides difficile R20291 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.97 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_48170.png

Downloads & links

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Map

FileDownload / File: emd_48170.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
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: 0.06
Minimum - Maximum-0.31464475 - 0.91338784
Average (Standard dev.)-0.0013193096 (±0.027478557)
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: #1

Fileemd_48170_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_48170_half_map_2.map
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

EntireName: Clostridioides difficile Transferase Component B
Components
  • Complex: Clostridioides difficile Transferase Component B
    • Protein or peptide: Adp-ribosyltransferase binding component

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Supramolecule #1: Clostridioides difficile Transferase Component B

SupramoleculeName: Clostridioides difficile Transferase Component B / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Molecular weightTheoretical: 75 KDa

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Macromolecule #1: Adp-ribosyltransferase binding component

MacromoleculeName: Adp-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKLL DKDKSDVKSI RWTGRIIPSK DGEYTLSTDR DDVLMQVNTE STISNTLKVN MKKGKEYKVR IELQDKNLGS IDNLSSPNLY ...String:
MKIQMRNKKV LSFLTLTAIV SQALVYPVYA QTSTSNHSNK KKEIVNEDIL PNNGLMGYYF TDEHFKDLKL MAPIKDGNLK FEEKKVDKLL DKDKSDVKSI RWTGRIIPSK DGEYTLSTDR DDVLMQVNTE STISNTLKVN MKKGKEYKVR IELQDKNLGS IDNLSSPNLY WELDGMKKII PEENLFLRDY SNIEKDDPFI PNNNFFDPKL MSDWEDEDLD TDNDNIPDSY ERNGYTIKDL IAVKWEDSFA EQGYKKYVSN YLESNTAGDP YTDYEKASGS FDKAIKTEAR DPLVAAYPIV GVGMEKLIIS TNEHASTDQG KTVSRATTNS KTESNTAGVS VNVGYQNGFT ANVTTNYSHT TDNSTAVQDS NGESWNTGLS INKGESAYIN ANVRYYNTGT APMYKVTPTT NLVLDGDTLS TIKAQENQIG NNLSPGDTYP KKGLSPLALN TMDQFSSRLI PINYDQLKKL DAGKQIKLET TQVSGNFGTK NSSGQIVTEG NSWSDYISQI DSISASIILD TENESYERRV TAKNLQDPED KTPELTIGEA IEKAFGATKK DGLLYFNDIP IDESCVELIF DDNTANKIKD SLKTLSDKKI YNVKLERGMN ILIKTPTYFT NFDDYNNYPS TWSNVNTTNQ DGLQGSANKL NGETKIKIPM SELKPYKRYV FSGYSKDPLT SNSIIVKIKA KEEKTDYLVP EQGYTKFSYE FETTEKDSSN IEITLIGSGT TYLDNLSITE LNSTPEILDE PEVKIPTDQE IMDAHKIYFA DLNFNPSTGN TYINGMYFAP TQTNKEALDY IQKYRVEATL QYSGFKDIGT KDKEMRNYLG DPNQPKTNYV NLRSYFTGGE NIMTYKKLRI YAITPDDREL LVLSVD

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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
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec.
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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 6.97 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 49147
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. v4)

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