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- EMDB-28207: Clostridioides difficile binary toxin translocase CDTb double mut... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28207
TitleClostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A
Map data
Sample
  • Complex: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant
    • Protein or peptide: ADP-ribosyltransferase binding component
  • Ligand: CALCIUM ION
Keywordstranslocase / binary toxin / calcium / 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: 3.56 Å
AuthorsAbeyawardhane DL / Pozharski E
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R56AI152397 United States
CitationJournal: To Be Published
Title: Calcium-mediated Pore Formation of Clostridioides difficile Binary Toxin
Authors: Abeyawardhane DL / Adipietro KA / Ruiz RG / Varney KM / Rustandi RR / Silin VI / Pozharski E / Weber DJ
History
DepositionSep 21, 2022-
Header (metadata) releaseSep 27, 2023-
Map releaseSep 27, 2023-
UpdateSep 27, 2023-
Current statusSep 27, 2023Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_28207.png

Downloads & links

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Map

FileDownload / File: emd_28207.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å		0.89 Å/pix.
x 400 pix.
= 355.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.889 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.5
Minimum - Maximum-1.6839105 - 3.0829937
Average (Standard dev.)0.0008781474 (±0.068554394)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 355.6 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_28207_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_28207_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 : Single heptamer of Clostridioides difficile binary toxin transloc...

EntireName: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant
Components
  • Complex: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant
    • Protein or peptide: ADP-ribosyltransferase binding component
  • Ligand: CALCIUM ION

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Supramolecule #1: Single heptamer of Clostridioides difficile binary toxin transloc...

SupramoleculeName: Single heptamer of Clostridioides difficile binary toxin translocase CDTb D623A D734A double mutant
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: R20291

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Macromolecule #1: ADP-ribosyltransferase binding component

MacromoleculeName: ADP-ribosyltransferase binding component / type: protein_or_peptide / ID: 1 / Number of copies: 7 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria) / Strain: R20291
Molecular weightTheoretical: 74.591078 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 TPTYFTNFAD YNNYPSTWSN VNTTNQDGLQ GSANKLNGET KIKIPMSELK PYKRYVFSGY SKDPLTSNSI IVKIK AKEE KTDYLVPEQG YTKFSYEFET TEKDSSNIEI TLIGSGTTYL ANLSITELNS 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: 14 / 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: 7
Component:
ConcentrationFormulaName
15.0 mMC8H18N2O4SHEPES
150.0 mMNaClsodium chloride
GridModel: Quantifoil / Material: COPPER / Support film - Material: CARBON / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Calibrated defocus max: 2.7 µm / Calibrated defocus min: 0.5 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN

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Image processing

Particle selectionNumber selected: 993305
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uwr

Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.56 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 78587
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6uwr


Chain - Chain ID: A / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 2

Initial modelPDB ID:

6uwr


Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 3

Initial modelPDB ID:

6uwr


Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 4

Initial modelPDB ID:

6uwr


Chain - Chain ID: D / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 5

Initial modelPDB ID:

6uwr


Chain - Chain ID: E / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 6

Initial modelPDB ID:

6uwr


Chain - Chain ID: F / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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Atomic model buiding 7

Initial modelPDB ID:

6uwr


Chain - Chain ID: G / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementProtocol: AB INITIO MODEL
Output model

PDB-8ekm:
Clostridioides difficile binary toxin translocase CDTb double mutant - D623A D734A

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