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- EMDB-28206: Clostridioides difficile binary toxin translocase CDTb wild-type ... -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-28206
TitleClostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1
Map data
Sample
  • Complex: Single heptamer (class 1) of Clostridioides difficile binary toxin translocase CDTb wild-type after depletion of calcium from RBD1
    • Protein or peptide: ADP-ribosyltransferase binding componentPoly (ADP-ribose) polymerase
  • Ligand: CALCIUM IONCalcium
Keywordstranslocase / binary toxin / pore-forming / TOXIN
Function / homology
Function and homology information


protein homooligomerization / transferase activity / extracellular region
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: 3.06 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_28206.png

Downloads & links

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Map

FileDownload / File: emd_28206.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.889 Å
Density
Contour LevelBy AUTHOR: 0.228
Minimum - Maximum-0.6247456 - 1.1988856
Average (Standard dev.)0.0011245409 (±0.051684257)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 227.584 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_28206_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_28206_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 (class 1) of Clostridioides difficile binary toxi...

EntireName: Single heptamer (class 1) of Clostridioides difficile binary toxin translocase CDTb wild-type after depletion of calcium from RBD1
Components
  • Complex: Single heptamer (class 1) of Clostridioides difficile binary toxin translocase CDTb wild-type after depletion of calcium from RBD1
    • Protein or peptide: ADP-ribosyltransferase binding componentPoly (ADP-ribose) polymerase
  • Ligand: CALCIUM IONCalcium

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Supramolecule #1: Single heptamer (class 1) of Clostridioides difficile binary toxi...

SupramoleculeName: Single heptamer (class 1) of Clostridioides difficile binary toxin translocase CDTb wild-type after depletion of calcium from RBD1
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: 74.679086 KDa
Recombinant expressionOrganism: Spodoptera frugiperda (fall armyworm)
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: 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 chloridesodium chloride
GridModel: Quantifoil / Material: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS GLACIOS
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 FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 45000
Sample stageCooling holder cryogen: NITROGEN
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2

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Image processing

Particle selectionNumber selected: 1109860
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

6uwr

Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final 3D classificationSoftware - Name: cryoSPARC (ver. 3.3.2)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 3.3.2)
Final reconstructionApplied symmetry - Point group: C7 (7 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.06 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.3.2) / Number images used: 33531
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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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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-8ekl:
Clostridioides difficile binary toxin translocase CDTb wild-type after calcium depletion from receptor binding domain 1 (RBD1) - Class 1

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