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- EMDB-13574: High-resolution structure of native toxin A from Clostridioides d... -

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Basic information

Entry
Database: EMDB / ID: EMD-13574
TitleHigh-resolution structure of native toxin A from Clostridioides difficile
Map data
Sample
  • Organelle or cellular component: Clostridioides difficile Toxin A
    • Protein or peptide: Toxin A
  • Ligand: ZINC ION
Keywordsglucosyltransferase / TOXIN
Function / homology
Function and homology information


host cell cytosol / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / plasma membrane
Similarity search - Function
TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. ...TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.83 Å
AuthorsBoesen T / Joergensen R
Funding support Denmark, 1 items
OrganizationGrant numberCountry
Novo Nordisk FoundationNNF17OC0029548 Denmark
CitationJournal: EMBO Rep / Year: 2022
Title: High-resolution structure of native toxin A from Clostridioides difficile.
Authors: Aria Aminzadeh / Christian Engelbrecht Larsen / Thomas Boesen / René Jørgensen /
Abstract: Clostridioides difficile infections have emerged as the leading cause of healthcare-associated infectious diarrhea. Disease symptoms are mainly caused by the virulence factors, TcdA and TcdB, which ...Clostridioides difficile infections have emerged as the leading cause of healthcare-associated infectious diarrhea. Disease symptoms are mainly caused by the virulence factors, TcdA and TcdB, which are large homologous multidomain proteins. Here, we report a 2.8 Å resolution cryo-EM structure of native TcdA, unveiling its conformation at neutral pH. The structure uncovers the dynamic movement of the CROPs domain which is induced in response to environmental acidification. Furthermore, the structure reveals detailed information about the interaction area between the CROPs domain and the tip of the delivery and receptor-binding domain, which likely serves to shield the C-terminal part of the hydrophobic pore-forming region from solvent exposure. Similarly, extensive interactions between the globular subdomain and the N-terminal part of the pore-forming region suggest that the globular subdomain shields the upper part of the pore-forming region from exposure to the surrounding solvent. Hence, the TcdA structure provides insights into the mechanism of preventing premature unfolding of the pore-forming region at neutral pH, as well as the pH-induced inter-domain dynamics.
History
DepositionSep 8, 2021-
Header (metadata) releaseDec 8, 2021-
Map releaseDec 8, 2021-
UpdateJul 17, 2024-
Current statusJul 17, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0359
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0359
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7pog
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7pog
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13574.png

Downloads & links

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Map

FileDownload / File: emd_13574.map.gz / Format: CCP4 / Size: 1.1 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.64 Å/pix.
x 656 pix.
= 419.84 Å		0.64 Å/pix.
x 656 pix.
= 419.84 Å		0.64 Å/pix.
x 656 pix.
= 419.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.64 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0359 / Movie #1: 0.0359
Minimum - Maximum-0.089972176 - 0.2386812
Average (Standard dev.)-0.000069181566 (±0.0051932493)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions656656656
Spacing656656656
CellA=B=C: 419.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.640.640.64
M x/y/z656656656
origin x/y/z0.0000.0000.000
length x/y/z419.840419.840419.840
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS656656656
D min/max/mean-0.0900.239-0.000

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Supplemental data

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Sample components

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Entire : Clostridioides difficile Toxin A

EntireName: Clostridioides difficile Toxin A
Components
  • Organelle or cellular component: Clostridioides difficile Toxin A
    • Protein or peptide: Toxin A
  • Ligand: ZINC ION

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Supramolecule #1: Clostridioides difficile Toxin A

SupramoleculeName: Clostridioides difficile Toxin A / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Clostridioides difficile (bacteria)

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Macromolecule #1: Toxin A

MacromoleculeName: Toxin A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 308.613188 KDa
SequenceString: MSLISKEELI KLAYSIRPRE NEYKTILTNL DEYNKLTTNN NENKYLQLKK LNESIDVFMN KYKNSSRNRA LSNLKKDILK EVILIKNSN TSPVEKNLHF VWIGGEVSDI ALEYIKQWAD INAEYNIKLW YDSEAFLVNT LKKAIVESST TEALQLLEEE I QNPQFDNM ...String:
MSLISKEELI KLAYSIRPRE NEYKTILTNL DEYNKLTTNN NENKYLQLKK LNESIDVFMN KYKNSSRNRA LSNLKKDILK EVILIKNSN TSPVEKNLHF VWIGGEVSDI ALEYIKQWAD INAEYNIKLW YDSEAFLVNT LKKAIVESST TEALQLLEEE I QNPQFDNM KFYKKRMEFI YDRQKRFINY YKSQINKPTV PTIDDIIKSH LVSEYNRDET LLESYRTNSL RKINSNHGID IR ANSLFTE QELLNIYSQE LLNRGNLAAA SDIVRLLALK NFGGVYLDVD MLPGIHSDLF KTIPRPSSIG LDRWEMIKLE AIM KYKKYI NNYTSENFDK LDQQLKDNFK LIIESKSEKS EIFSKLENLN VSDLEIKIAF ALGSVINQAL ISKQGSYLTN LVIE QVKNR YQFLNQHLNP AIESDNNFTD TTKIFHDSLF NSATAENSMF LTKIAPYLQV GFMPEARSTI SLSGPGAYAS AYYDF INLQ ENTIEKTLKA SDLIEFKFPE NNLSQLTEQE INSLWSFDQA SAKYQFEKYV RDYTGGSLSE DNGVDFNKNT ALDKNY LLN NKIPSNNVEE AGSKNYVHYI IQLQGDDISY EATCNLFSKN PKNSIIIQRN MNESAKSYFL SDDGESILEL NKYRIPE RL KNKEKVKVTF IGHGKDEFNT SEFARLSVDS LSNEISSFLD TIKLDISPKN VEVNLLGCNM FSYDFNVEET YPGKLLLS I MDKITSTLPD VNKDSITIGA NQYEVRINSE GRKELLAHSG KWINKEEAIM SDLSSKEYIF FDSIDNKLKA KSKNIPGLA SISEDIKTLL LDASVSPDTK FILNNLKLNI ESSIGDYIYY EKLEPVKNII HNSIDDLIDE FNLLENVSDE LYELKKLNNL DEKYLISFE DISKNNSTYS VRFINKSNGE SVYVETEKEI FSKYSEHITK EISTIKNSII TDVNGNLLDN IQLDHTSQVN T LNAAFFIQ SLIDYSSNKD VLNDLSTSVK VQLYAQLFST GLNTIYDSIQ LVNLISNAVN DTINVLPTIT EGIPIVSTIL DG INLGAAI KELLDEHDPL LKKELEAKVG VLAINMSLSI AATVASIVGI GAEVTIFLLP IAGISAGIPS LVNNELILHD KAT SVVNYF NHLSESKEYG PLKTEDDKIL VPIDDLVISE IDFNNNSIKL GTCNILAMEG GSGHTVTGNI DHFFSSPYIS SHIP SLSVY SAIGIKTENL DFSKKIMMLP NAPSRVFWWE TGAVPGLRSL ENNGTKLLDS IRDLYPGKFY WRFYAFFDYA ITTLK PVYE DTNTKIKLDK DTRNFIMPTI TTDEIRNKLS YSFDGAGGTY SLLLSSYPIS MNINLSKDDL WIFNIDNEVR EISIEN GTI KKGNLIEDVL SKIDINKNKL IIGNQTIDFS GDIDNKDRYI FLTCELDDKI SLIIEINLVA KSYSLLLSGD KNYLISN LS NTIEKINTLG LDSKNIAYNY TDESNNKYFG AISKTSQKSI IHYKKDSKNI LEFYNGSTLE FNSKDFIAED INVFMKDD I NTITGKYYVD NNTDKSIDFS ISLVSKNQVK VNGLYLNESV YSSYLDFVKN SDGHHNTSNF MNLFLNNISF WKLFGFENI NFVIDKYFTL VGKTNLGYVE FICDNNKNID IYFGEWKTSS SKSTIFSGNG RNVVVEPIYN PDTGEDISTS LDFSYEPLYG IDRYINKVL IAPDLYTSLI NINTNYYSNE YYPEIIVLNP NTFHKKVNIN LDSSSFEYKW STEGSDFILV RYLEESNKKI L QKIRIKGI LSNTQSFNKM SIDFKDIKKL SLGYIMSNFK SFNSENELDR DHLGFKIIDN KTYYYDEDSK LVKGLININN SL FYFDPIE SNLVTGWQTI NGKKYYFDIN TGAASTSYKI INGKHFYFNN NGVMQLGVFK GPDGFEYFAP ANTQNNNIEG QAI VYQSKF LTLNGKKYYF DNDSKAVTGW RIINNEKYYF NPNNAIAAVG LQVIDNNKYY FNPDTAIISK GWQTVNGSRY YFDT DTAIA FNGYKTIDGK HFYFDSDCVV KIGVFSGSNG FEYFAPANTY NNNIEGQAIV YQSKFLTLNG KKYYFDNNSK AVTGW QTID SKKYYFNTNT AEAATGWQTI DGKKYYFNTN TAEAATGWQT IDGKKYYFNT NTSIASTGYT IINGKYFYFN TDGIMQ IGV FKVPNGFEYF APANTHNNNI EGQAILYQNK FLTLNGKKYY FGSDSKAITG WQTIDGKKYY FNPNNAIAAT HLCTINN DK YYFSYDGILQ NGYITIERNN FYFDANNESK MVTGVFKGPN GFEYFAPANT HNNNIEGQAI VYQNKFLTLN GKKYYFDN D SKAVTGWQTI DSKKYYFNLN TAVAVTGWQT IDGEKYYFNL NTAEAATGWQ TIDGKRYYFN TNTYIASTGY TIINGKHFY FNTDGIMQIG VFKGPDGFEY FAPANTHNNN IEGQAILYQN KFLTLNGKKY YFGSDSKAVT GLRTIDGKKY YFNTNTAVAV TGWQTINGK KYYFNTNTYI ASTGYTIISG KHFYFNTDGI MQIGVFKGPD GFEYFAPANT DANNIEGQAI RYQNRFLYLH D NIYYFGND SKAATGWATI DGNRYYFEPN TAMGANGYKT IDNKNFYFRN GLPQIGVFKG PNGFEYFAPA NTDANNIDGQ AI RYQNRFL HLLGKIYYFG NNSKAVTGWQ TINSKVYYFM PDTAMAAAGG LFEIDGVIYF FGVDGVKAPG IYG

UniProtKB: Toxin A

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Macromolecule #2: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 2 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.83 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 900000
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL
Output model

PDB-7pog:
High-resolution structure of native toxin A from Clostridioides difficile

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