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- EMDB-48177: Clostridioides difficile Transferase B Component Hexamer -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-48177
TitleClostridioides difficile Transferase B Component Hexamer
Map dataCDTb hexamer map.
Sample
  • Complex: Clostridioides difficile Transferase Component B
KeywordsToxin / Clostridioides / Iota / ADP-ribosyltransferase
Biological speciesClostridioides difficile R20291 (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.05 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: To Be Published
Title: Oligomerization of the Clostridioides difficile Transferase B Component Proceeds through a Stepwise Mechanism In Vitro
Authors: Sheedlo MJ / Mullard RM
History
DepositionDec 5, 2024-
Header (metadata) releaseJul 16, 2025-
Map releaseJul 16, 2025-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48177.png

Downloads & links

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Map

FileDownload / File: emd_48177.map.gz / Format: CCP4 / Size: 149.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCDTb hexamer 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: 0.175
Minimum - Maximum-0.29744375 - 0.6890873
Average (Standard dev.)0.0046852217 (±0.038901057)
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 hexamer half map A.

Fileemd_48177_half_map_1.map
AnnotationCDTb hexamer half map A.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: CDTb hexamer half map B.

Fileemd_48177_half_map_2.map
AnnotationCDTb hexamer half map B.
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

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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: #1-#2
Source (natural)Organism: Clostridioides difficile R20291 (bacteria)
Molecular weightTheoretical: 450 KDa

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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: 12.05 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 2688
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: AB INITIO MODEL

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