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- EMDB-44419: Structure of Clostridioides difficile Component A (50-463) in Com... -

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Basic information

Entry
Database: EMDB / ID: EMD-44419
TitleStructure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer
Map data
Sample
  • Complex: Clostridioides difficile Transferase component A in complex with Clostridioides difficile Transferase component B
    • Protein or peptide: ADP-ribosyltransferase binding component
    • Protein or peptide: ADP-ribosyltransferase enzymatic component
  • Ligand: CALCIUM ION
KeywordsClostridioides / difficile / toxin / CDT / TRANSFERASE
Function / homology
Function and homology information


Transferases; Glycosyltransferases; Pentosyltransferases / protein homooligomerization / transferase activity / nucleotide binding / extracellular region / metal ion binding / identical protein binding
Similarity search - Function
Binary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / 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 ...Binary exotoxin A, clostridial type / ADP ribosyltransferase / ADP-ribosyltransferase exoenzyme / 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 / Toxin-related mono-ADP-ribosyltransferase (TR mART) core domain profile. / PA14 domain / PA14 / PA14 domain
Similarity search - Domain/homology
ADP-ribosyltransferase binding component / ADP-ribosyltransferase enzymatic component
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: Structure of Clostridioides difficile Component A (50-463) in Complex with a CDTb Oligomer
Authors: Sheedlo MJ / Mullard RM
History
DepositionApr 5, 2024-
Header (metadata) releaseNov 27, 2024-
Map releaseNov 27, 2024-
UpdateMay 21, 2025-
Current statusMay 21, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_44419.png

Downloads & links

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Map

FileDownload / File: emd_44419.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.)
0.65 Å/pix.
x 340 pix.
= 221. Å		0.65 Å/pix.
x 340 pix.
= 221. Å		0.65 Å/pix.
x 340 pix.
= 221. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.65 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.0540575 - 1.7252381
Average (Standard dev.)0.0055412534 (±0.06410685)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions340340340
Spacing340340340
CellA=B=C: 220.99998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_44419_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_44419_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 A in complex with ...

EntireName: Clostridioides difficile Transferase component A in complex with Clostridioides difficile Transferase component B
Components
  • Complex: Clostridioides difficile Transferase component A in complex with Clostridioides difficile Transferase component B
    • Protein or peptide: ADP-ribosyltransferase binding component
    • Protein or peptide: ADP-ribosyltransferase enzymatic component
  • Ligand: CALCIUM ION

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Supramolecule #1: Clostridioides difficile Transferase component A in complex with ...

SupramoleculeName: Clostridioides difficile Transferase component A in complex with Clostridioides difficile Transferase component B
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Clostridioides difficile (bacteria)

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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)
Molecular weightTheoretical: 94.289367 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MEIVNEDILP NNGLMGYYFT DEHFKDLKLM APIKDGNLKF EEKKVDKLLD KDKSDVKSIR WTGRIIPSKD GEYTLSTDRD DVLMQVNTE STISNTLKVN MKKGKEYKVR IELQDKNLGS IDNLSSPNLY WELDGMKKII PEENLFLRDY SNIEKDDPFI P NNNFFDPK ...String:
MEIVNEDILP NNGLMGYYFT DEHFKDLKLM APIKDGNLKF EEKKVDKLLD KDKSDVKSIR WTGRIIPSKD GEYTLSTDRD DVLMQVNTE STISNTLKVN MKKGKEYKVR IELQDKNLGS IDNLSSPNLY WELDGMKKII PEENLFLRDY SNIEKDDPFI P NNNFFDPK LMSDWEDEDL DTDNDNIPDS YERNGYTIKD LIAVKWEDSF AEQGYKKYVS NYLESNTAGD PYTDYEKASG SF DKAIKTE ARDPLVAAYP IVGVGMEKLI ISTNEHASTD QGKTVSRATT NSKTESNTAG VSVNVGYQNG FTANVTTNYS HTT DNSTAV QDSNGESWNT GLSINKGESA YINANVRYYN TGTAPMYKVT PTTNLVLDGD TLSTIKAQEN QIGNNLSPGD TYPK KGLSP LALNTMDQFS SRLIPINYDQ LKKLDAGKQI KLETTQVSGN FGTKNSSGQI VTEGNSWSDY ISQIDSISAS IILDT ENES YERRVTAKNL QDPEDKTPEL TIGEAIEKAF GATKKDGLLY FNDIPIDESC VELIFDDNTA NKIKDSLKTL SDKKIY NVK LERGMNILIK TPTYFTNFDD YNNYPSTWSN VNTTNQDGLQ GSANKLNGET KIKIPMSELK PYKRYVFSGY SKDPLTS NS IIVKIKAKEE KTDYLVPEQG YTKFSYEFET TEKDSSNIEI TLIGSGTTYL DNLSITELNS TPEILDEPEV KIPTDQEI M DAHKIYFADL NFNPSTGNTY INGMYFAPTQ TNKEALDYIQ KYRVEATLQY SGFKDIGTKD KEMRNYLGDP NQPKTNYVN LRSYFTGGEN IMTYKKLRIY AITPDDRELL VLSVD

UniProtKB: ADP-ribosyltransferase binding component

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Macromolecule #2: ADP-ribosyltransferase enzymatic component

MacromoleculeName: ADP-ribosyltransferase enzymatic component / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 47.626613 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRNA ISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD EKPTPLLMHL K LPRNTGML ...String:
KAPIERPEDF LKDKEKAKEW ERKEAERIEQ KLERSEKEAL ESYKKDSVEI SKYSQTRNYF YDYQIEANSR EKEYKELRNA ISKNKIDKP MYVYYFESPE KFAFNKVIRT ENQNEISLEK FNEFKETIQN KLFKQDGFKD ISLYEPGKGD EKPTPLLMHL K LPRNTGML PYTNTNNVST LIEQGYSIKI DKIVRIVIDG KHYIKAEASV VSSLDFKDDV SKGDSWGKAN YNDWSNKLTP NE LADVNDY MRGGYTAINN YLISNGPVNN PNPELDSKIT NIENALKREP IPTNLTVYRR SGPQEFGLTL TSPEYDFNKL ENI DAFKSK WEGQALSYPN FISTSIGSVN MSAFAKRKIV LRITIPKGSP GAYLSAIPGY AGEYEVLLNH GSKFKINKID SYKD GTITK LIVDATLIP

UniProtKB: ADP-ribosyltransferase enzymatic component

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Macromolecule #3: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 3 / 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: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 43726
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)

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