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- EMDB-24248: Partial C. difficile TcdB and CSPG4 fragment -

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Basic information

Entry
Database: EMDB / ID: EMD-24248
TitlePartial C. difficile TcdB and CSPG4 fragment
Map dataPartial C. difficile TcdB with CSPG4 (410-560)
Sample
  • Complex: The complex of TcdB and CSPG4 fragment
    • Organelle or cellular component: Ternary structure of C-terminus of CSPG4 domain 1
      • Protein or peptide: Chondroitin sulfate proteoglycan 4
    • Organelle or cellular component: Ternary structure of Clostridium difficile TcdB
      • Protein or peptide: Toxin B
Function / homology
Function and homology information


Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / substrate-dependent cell migration ...Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / substrate-dependent cell migration / A tetrasaccharide linker sequence is required for GAG synthesis / glial cell migration / tissue remodeling / ruffle assembly / glucosyltransferase activity / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / coreceptor activity / cysteine-type peptidase activity / ruffle / lysosomal lumen / host cell endosome membrane / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / toxin activity / angiogenesis / collagen-containing extracellular matrix / positive regulation of MAPK cascade / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / intracellular signal transduction / apical plasma membrane / focal adhesion / lipid binding / protein kinase binding / host cell plasma membrane / cell surface / proteolysis / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / plasma membrane
Similarity search - Function
CSPG repeat / : / Cadherin-like / CSPG repeat 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 ...CSPG repeat / : / Cadherin-like / CSPG repeat 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 / Laminin G domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Laminin G domain profile. / Choline-binding repeat / Laminin G domain / Putative cell wall binding repeat / Laminin G domain / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Toxin B / Chondroitin sulfate proteoglycan 4
Similarity search - Component
Biological speciesClostridioides difficile (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJiang M / Zhang J
Funding support United States, 2 items
OrganizationGrant numberCountry
Welch Foundation United States
National Institutes of Health/National Center for Research Resources (NIH/NCRR) United States
CitationJournal: To Be Published
Title: Structural Basis for Receptor Recognition of Clostridium difficile Toxin B and its Dissociation upon Acidification
Authors: Jiang M / Zhang J
History
DepositionJun 16, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 3
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n8x
  • Surface level: 3
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24248.png

Downloads & links

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Map

FileDownload / File: emd_24248.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPartial C. difficile TcdB with CSPG4 (410-560)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 180 pix.
= 203.4 Å		1.13 Å/pix.
x 180 pix.
= 203.4 Å		1.13 Å/pix.
x 180 pix.
= 203.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.13 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0 / Movie #1: 3
Minimum - Maximum-14.996973 - 37.40654
Average (Standard dev.)0.02329624 (±0.77337414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions180180180
Spacing180180180
CellA=B=C: 203.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z180180180
origin x/y/z0.0000.0000.000
length x/y/z203.400203.400203.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS180180180
D min/max/mean-14.99737.4070.023

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Supplemental data

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Sample components

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Entire : The complex of TcdB and CSPG4 fragment

EntireName: The complex of TcdB and CSPG4 fragment
Components
  • Complex: The complex of TcdB and CSPG4 fragment
    • Organelle or cellular component: Ternary structure of C-terminus of CSPG4 domain 1
      • Protein or peptide: Chondroitin sulfate proteoglycan 4
    • Organelle or cellular component: Ternary structure of Clostridium difficile TcdB
      • Protein or peptide: Toxin B

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Supramolecule #1: The complex of TcdB and CSPG4 fragment

SupramoleculeName: The complex of TcdB and CSPG4 fragment / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
Molecular weightExperimental: 250 KDa

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Supramolecule #2: Ternary structure of C-terminus of CSPG4 domain 1

SupramoleculeName: Ternary structure of C-terminus of CSPG4 domain 1 / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Homo sapiens (human)

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Supramolecule #3: Ternary structure of Clostridium difficile TcdB

SupramoleculeName: Ternary structure of Clostridium difficile TcdB / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Clostridioides difficile (bacteria)
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)

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Macromolecule #1: Chondroitin sulfate proteoglycan 4

MacromoleculeName: Chondroitin sulfate proteoglycan 4 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.565927 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
LPEPCVPEPG LPPVFANFTQ LLTISPLVVA EGGTAWLEWR HVQPTLDLME AELRKSQVLF SVTRGARHGE LELDIPGAQA RKMFTLLDV VNRKARFIHD GSEDTSDQLV LEVSVTARVP MPSCLRRGQT YLLPIQVNPV N

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Macromolecule #2: Toxin B

MacromoleculeName: Toxin B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 169.479141 KDa
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
SequenceString: KIAFNSKGII NQGLISVKDS YCSNLIVKQI ENRYKILNNS LNPAISEDND FNTTTNTFID SIMAEANADN GRFMMELGKY LRVGFFPDV KTTINLSGPE AYAAAYQDLL MFKEGSMNIH LIEADLRNFE ISKTNISQST EQEMASLWSF DDARAKAQFE E YKRNYFEG ...String:
KIAFNSKGII NQGLISVKDS YCSNLIVKQI ENRYKILNNS LNPAISEDND FNTTTNTFID SIMAEANADN GRFMMELGKY LRVGFFPDV KTTINLSGPE AYAAAYQDLL MFKEGSMNIH LIEADLRNFE ISKTNISQST EQEMASLWSF DDARAKAQFE E YKRNYFEG SLGEDDNLDF SQNIVVDKEY LLEKISSLAR SSERGYIHYI VQLQGDKISY EAACNLFAKT PYDSVLFQKN IE DSEIAYY YNPGDGEIQE IDKYKIPSII SDRPKIKLTF IGHGKDEFNT DIFAGFDVDS LSTEIEAAID LAKEDISPKS IEI NLLGCN MFSYSINVEE TYPGKLLLKV KDKISELMPS ISQDSIIVSA NQYEVRINSE GRRELLDHSG EWINKEESII KDIS SKEYI SFNPKENKIT VKSKNLPELS TLLQEIRNNS NSSDIELEEK VMLTECEINV ISNIDTQIVE ERIEEAKNLT SDSIN YIKD EFKLIESISD ALCDLKQQNE LEDSHFISFE DISETDEGFS IRFINKETGE SIFVETEKTI FSEYANHITE EISKIK GTI FDTVNGKLVK KVNLDTTHEV NTLNAAFFIQ SLIEYNSSKE SLSNLSVAMK VQVYAQLFST GLNTITDAAK VVELVST AL DETIDLLPTL SEGLPIIATI IDGVSLGAAI KELSETSDPL LRQEIEAKIG IMAVNLTTAT TAIITSSLGI ASGFSILL V PLAGISAGIP SLVNNELVLR DKATKVVDYF KHVSLVETEG VFTLLDDKIM MPQDDLVISE IDFNNNSIVL GKCEIWRME GGSGHTVTDD IDHFFSAPSI TYREPHLSIY DVLEVQKEEL DLSKDLMVLP NAPNRVFAWE TGWTPGLRSL ENDGTKLLDR IRDNYEGEF YWRYFAFIAD ALITTLKPRY EDTNIRINLD SNTRSFIVPI ITTEYIREKL SYSFYGSGGT YALSLSQYNM G INIELSES DVWIIDVDNV VRDVTIESDK IKKGDLIEGI LSTLSIEENK IILNSHEINF SGEVNGSNGF VSLTFSILEG IN AIIEVDL LSKSYKLLIS GELKILMLNS NHIQQKIDYI GFNSELQKNI PYSFVDSEGK ENGFINGSTK EGLFVSELPD VVL ISKVYM DDSKPSFGYY SNNLKDVKVI TKDNVNILTG YYLKDDIKIS LSLTLQDEKT IKLNSVHLDE SGVAEILKFM NRKG NTNTS DSLMSFLESM NIKSIFVNFL QSNIKFILDA NFIISGTTSI GQFEFICDEN DNIQPYFIKF NTLETNYTLY VGNRQ NMIV EPNYDLDDSG DISSTVINFS QKYLYGIDSC VNKVVISPNI YTDEINITPV YETNNTYPEV IVLDANYINE KINVNI NDL SIRYVWSNDG NDFILMSTSE ENKVSQVKIR FVNVFKDKTL ANKLSFNFSD KQDVPVSEII LSFTPSYYED GLIGYDL GL VSLYNEKFYI NNFGMMVSGL IYINDSLYYF KPPVNNLITG FVTVGDDKYY FNPINGGAAS I

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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
GridMaterial: COPPER / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 40.0 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: OTHER / Details: model prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 470301
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7n8x:
Partial C. difficile TcdB and CSPG4 fragment

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