[English] 日本語
Yorodumi
- EMDB-48707: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48707
TitleClostridioides difficile Toxin A with mCDIFA-248-25 Fab
Map dataClostridioides difficile Toxin A with mCDIFA-248-25 Fab
Sample
  • Complex: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab
    • Protein or peptide: Toxin A
    • Protein or peptide: mCDIFA-248-25 Fab Heavy Chain
    • Protein or peptide: mCDIFA-248-25 Fab Light Chain
KeywordsToxin A / TcdA / C.diff / Complex / TRANSFERASE / TOXIN-IMMUNE SYSTEM complex
Function / homology
Function and homology information


host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / glycosyltransferase activity / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / metal ion binding / 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) / Mus musculus (house mouse)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsHuynh KW / Ammirati M / Kroh HK / Lacy DB / Han S
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Mouse monoclonal antibodies against Clostridioides difficile toxins TcdA and TcdB target diverse epitopes for neutralization
Authors: Kroh HK / Jensen JL / Wellnitz S / Park JJ / Esadze A / Huynh KW / Ammirati M / Han S / Anderson AS / Lacy DB / Gribenko A
History
DepositionJan 17, 2025-
Header (metadata) releaseJul 9, 2025-
Map releaseJul 9, 2025-
UpdateJul 9, 2025-
Current statusJul 9, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_48707.png

Downloads & links

-
Map

FileDownload / File: emd_48707.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationClostridioides difficile Toxin A with mCDIFA-248-25 Fab
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.09 Å/pix.
x 360 pix.
= 390.96 Å		1.09 Å/pix.
x 360 pix.
= 390.96 Å		1.09 Å/pix.
x 360 pix.
= 390.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.086 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.097952746 - 0.16811228
Average (Standard dev.)0.000021128444 (±0.0042613694)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 390.96 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab Halfmap 1

Fileemd_48707_half_map_1.map
AnnotationClostridioides difficile Toxin A with mCDIFA-248-25 Fab Halfmap 1
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab Halfmap 2

Fileemd_48707_half_map_2.map
AnnotationClostridioides difficile Toxin A with mCDIFA-248-25 Fab Halfmap 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Clostridioides difficile Toxin A with mCDIFA-248-25 Fab

EntireName: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab
Components
  • Complex: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab
    • Protein or peptide: Toxin A
    • Protein or peptide: mCDIFA-248-25 Fab Heavy Chain
    • Protein or peptide: mCDIFA-248-25 Fab Light Chain

-
Supramolecule #1: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab

SupramoleculeName: Clostridioides difficile Toxin A with mCDIFA-248-25 Fab
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 358 KDa

-
Macromolecule #1: Toxin A

MacromoleculeName: Toxin A / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 308.331188 KDa
Recombinant expressionOrganism: Clostridioides difficile (bacteria)
SequenceString: MSLISKEELI KLAYSIRPRE NEYKTILTNL DEYNKLTTNN NENKYLQLKK LNESIDVFMN KYKTSSRNRA LSNLKKDILK EVILIKNSN TSPVEKNLHF VWIGGEVSDI ALEYIKQWAD INAEYNIKLW YDSEAFLVNT LKKAIVESST TEALQLLEEE I QNPQFDNM ...String:
MSLISKEELI KLAYSIRPRE NEYKTILTNL DEYNKLTTNN NENKYLQLKK LNESIDVFMN KYKTSSRNRA LSNLKKDILK EVILIKNSN TSPVEKNLHF VWIGGEVSDI ALEYIKQWAD INAEYNIKLW YDSEAFLVNT LKKAIVESST TEALQLLEEE I QNPQFDNM KFYKKRMEFI YDRQKRFINY YKSQINKPTV PTIDDIIKSH LVSEYNRDET VLESYRTNSL RKINSNHGID IR ANSLFTE QELLNIYSQE LLNRGNLAAA SDIVRLLALK NFGGVYLAVA MLPGIHSDLF KTISRPSSIG 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 VEVNLLGANM FSYDFNVEET YPGKLLLS I MDKITSTLPD VNKNSITIGA 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 NHLSESKKYG PLKTEDDKIL VPIDDLVISE IDFNNNSIKL GTCNILAMEG GSGHTVTGNI DHFFSSPSIS SHIP SLSIY SAIGIETENL DFSKKIMMLP NAPSRVFWWE TGAVPGLRSL ENDGTRLLDS IRDLYPGKFY WRFYAFFDYA ITTLK PVYE DTNIKIKLDK DTRNFIMPTI TTNEIRNKLS YSFDGAGGTY SLLLSSYPIS TNINLSKDDL WIFNIDNEVR EISIEN GTI KKGKLIKDVL SKIDINKNKL IIGNQTIDFS GDIDNKDRYI FLTCELDDKI SLIIEINLVA KSYSLLLSGD KNYLISN LS NIIEKINTLG LDSKNIAYNY TDESNNKYFG AISKTSQKSI IHYKKDSKNI LEFYNDSTLE FNSKDFIAED INVFMKDD I NTITGKYYVD NNTDKSIDFS ISLVSKNQVK VNGLYLNESV YSSYLDFVKN SDGHHNTSNF MNLFLDNISF 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 FNLVTGWQTI NGKKYYFDIN TGAALISYKI INGKHFYFNN DGVMQLGVFK GPDGFEYFAP ANTQNNNIEG QAI VYQSKF LTLNGKKYYF DNDSKAVTGW RIINNEKYYF NPNNAIAAVG LQVIDNNKYY FNPDTAIISK GWQTVNGSRY YFDT DTAIA FNGYKTIDGK HFYFDSDCVV KIGVFSTSNG FEYFAPANTY NNNIEGQAIV YQSKFLTLNG KKYYFDNNSK AVTGL QTID SKKYYFNTNT AEAATGWQTI DGKKYYFNTN TAEAATGWQT IDGKKYYFNT NTAIASTGYT IINGKHFYFN TDGIMQ IGV FKGPNGFEYF APANTDANNI EGQAILYQNE FLTLNGKKYY FGSDSKAVTG WRIINNKKYY FNPNNAIAAI HLCTINN DK YYFSYDGILQ NGYITIERNN FYFDANNESK MVTGVFKGPN GFEYFAPANT HNNNIEGQAI VYQNKFLTLN GKKYYFDN D SKAVTGWQTI DGKKYYFNLN TAEAATGWQT IDGKKYYFNL NTAEAATGWQ TIDGKKYYFN TNTFIASTGY TSINGKHFY FNTDGIMQIG VFKGPNGFEY FAPANTHNNN IEGQAILYQN KFLTLNGKKY YFGSDSKAVT GLRTIDGKKY YFNTNTAVAV TGWQTINGK KYYFNTNTSI ASTGYTIISG KHFYFNTDGI MQIGVFKGPD GFEYFAPANT DANNIEGQAI RYQNRFLYLH D NIYYFGNN SKAATGWVTI DGNRYYFEPN TAMGANGYKT IDNKNFYFRN GLPQIGVFKG SNGFEYFAPA NTDANNIEGQ AI RYQNRFL HLLGKIYYFG NNSKAVTGWQ TINGKVYYFM PDTAMAAAGG LFEIDGVIYF FGVDGVKAPG IYG

UniProtKB: Toxin A

-
Macromolecule #2: mCDIFA-248-25 Fab Heavy Chain

MacromoleculeName: mCDIFA-248-25 Fab Heavy Chain / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.654594 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: EVKLVESGGG LVKPGGSLKL SCAASGFTFS NYAMSWVRQT PEKRLEWVAA INGNGAKIYY PDTVKDRFTI SRDNAKNTLY LQMSSLRSE DTALYSCARQ YGFYAGSPYY FDYWGLGTTL TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP V TVTWNSGS ...String:
EVKLVESGGG LVKPGGSLKL SCAASGFTFS NYAMSWVRQT PEKRLEWVAA INGNGAKIYY PDTVKDRFTI SRDNAKNTLY LQMSSLRSE DTALYSCARQ YGFYAGSPYY FDYWGLGTTL TVSSAKTTPP SVYPLAPGSA AQTNSMVTLG CLVKGYFPEP V TVTWNSGS LSSGVHTFPA VLESDLYTLS SSVTVPSSPR PSETVTCNVA HPASSTKVDK KI

-
Macromolecule #3: mCDIFA-248-25 Fab Light Chain

MacromoleculeName: mCDIFA-248-25 Fab Light Chain / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Mus musculus (house mouse)
Molecular weightTheoretical: 23.726217 KDa
Recombinant expressionOrganism: Mus musculus (house mouse)
SequenceString: DIVMTQSHKF MSTSIGDRVS ITCKASQDVG TAVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTY FTLSISNVQS EDLADYFCQ QYSSYPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS ...String:
DIVMTQSHKF MSTSIGDRVS ITCKASQDVG TAVAWYQQKP GQSPKLLIYW ASTRHTGVPD RFTGSGSGTY FTLSISNVQS EDLADYFCQ QYSSYPLTFG AGTKLELKRA DAAPTVSIFP PSSEQLTSGG ASVVCFLNNF YPKDINVKWK IDGSERQNGV L NSWTDQDS KDSTYSMSST LTLTKDEYER HNSYTCEATH KTSTSPIVKS FNRNEC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration0.125 mg/mL
BufferpH: 7.5
Component:
ConcentrationNameFormula
25.0 mMTris
150.0 mMSodium ChlorideNaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 2511 / Average exposure time: 12.0 sec. / Average electron dose: 52.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 165000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 527742
CTF correctionSoftware - Name: CTFFIND (ver. 4) / Type: NONE
Startup modelType of model: OTHER / Details: Initial model was generated from RELION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 212265
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0) / Software - details: Initial Refinement
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.0) / Software - details: Final Refinement
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more