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- EMDB-24264: Full-length TcdB and CSPG4 (401-560) complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24264
TitleFull-length TcdB and CSPG4 (401-560) complex
Map dataFull-length TcdB and CSPG4 (401-560) complex
Sample
  • Complex: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
    • Organelle or cellular component: Ternary structure of CSPG4 (401-560)
      • Protein or peptide: Chondroitin sulfate proteoglycan 4
    • Organelle or cellular component: Ternary structure of Clostridium difficile TcdB
      • Protein or peptide: Toxin B
KeywordsTOXIN / SIGNALING PROTEIN-Hydrolase complex
Function / homology
Function and homology information


CS-GAG biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / DS-GAG biosynthesis / CS/DS degradation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / substrate-dependent cell migration / Defective B3GAT3 causes JDSSDHD ...CS-GAG biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / DS-GAG biosynthesis / CS/DS degradation / Defective B3GALT6 causes EDSP2 and SEMDJL1 / Defective B4GALT7 causes EDS, progeroid type / substrate-dependent cell migration / Defective B3GAT3 causes JDSSDHD / symbiont-mediated perturbation of host actin cytoskeleton via filamentous actin depolymerization / Glycosaminoglycan-protein linkage region biosynthesis / glial cell migration / tissue remodeling / ruffle assembly / glucosyltransferase activity / Differentiation of Keratinocytes in Interfollicular Epidermis in Mammalian Skin / positive regulation of peptidyl-tyrosine phosphorylation / Transferases; Glycosyltransferases; Hexosyltransferases / host cell cytosol / platelet-derived growth factor receptor signaling pathway / lamellipodium membrane / coreceptor activity / ruffle / cysteine-type peptidase activity / lysosomal lumen / host cell endosome membrane / Golgi lumen / : / toxin activity / angiogenesis / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / positive regulation of MAPK cascade / 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 / metal ion binding / membrane / plasma membrane
Similarity search - Function
CSPG repeat / : / Cadherin-like / CSPG repeat profile. / 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 ...CSPG repeat / : / Cadherin-like / CSPG repeat profile. / 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. / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Laminin G domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Laminin G domain / Laminin G domain / 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 speciesHomo sapiens (human) / Clostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsJiang M / Zhang J
Funding support United States, 1 items
OrganizationGrant numberCountry
Welch Foundation 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 18, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMay 28, 2025-
Current statusMay 28, 2025Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n9y
  • Surface level: 0.039
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24264.png

Downloads & links

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Map

FileDownload / File: emd_24264.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFull-length TcdB and CSPG4 (401-560) complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.13 Å/pix.
x 402 pix.
= 454.26 Å		1.13 Å/pix.
x 402 pix.
= 454.26 Å		1.13 Å/pix.
x 402 pix.
= 454.26 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: 0.039 / Movie #1: 0.039
Minimum - Maximum-0.0016779052 - 1.7417886
Average (Standard dev.)0.0007674187 (±0.019450704)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions402402402
Spacing402402402
CellA=B=C: 454.26 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.131.131.13
M x/y/z402402402
origin x/y/z0.0000.0000.000
length x/y/z454.260454.260454.260
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS402402402
D min/max/mean-0.0021.7420.001

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Supplemental data

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Sample components

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Entire : Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)

EntireName: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
Components
  • Complex: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
    • Organelle or cellular component: Ternary structure of CSPG4 (401-560)
      • 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: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)

SupramoleculeName: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Supramolecule #2: Ternary structure of CSPG4 (401-560)

SupramoleculeName: Ternary structure of CSPG4 (401-560) / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: 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)

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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

UniProtKB: Chondroitin sulfate proteoglycan 4

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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: 269.807219 KDa
Recombinant expressionOrganism: Priestia megaterium NBRC 15308 = ATCC 14581 (bacteria)
SequenceString: SLVNRKQLEK MANVRFRTQE DEYVAILDAL EEYHNMSENT VVEKYLKLKD INSLTDIYID TYKKSGRNKA LKKFKEYLVT EVLELKNNN LTPVEKNLHF VWIGGQINDT AINYINQWKD VNSDYNVNVF YDSNAFLINT LKKTVVESAI NDTLESFREN L NDPRFDYN ...String:
SLVNRKQLEK MANVRFRTQE DEYVAILDAL EEYHNMSENT VVEKYLKLKD INSLTDIYID TYKKSGRNKA LKKFKEYLVT EVLELKNNN LTPVEKNLHF VWIGGQINDT AINYINQWKD VNSDYNVNVF YDSNAFLINT LKKTVVESAI NDTLESFREN L NDPRFDYN KFFRKRMEII YDKQKNFINY YKAQREENPE LIIDDIVKTY LSNEYSKEID ELNTYIEESL NKITQNSGND VR NFEEFKN GESFNLYEQE LVERWNLAAA SDILRISALK EIGGMYLDVD MLPGIQPDLF ESIEKPSSVT VDFWEMTKLE AIM KYKEYI PEYTSEHFDM LDEEVQSSFE SVLASKSDKS EIFSSLGDME ASPLEVKIAF NSKGIINQGL ISVKDSYCSN LIVK QIENR YKILNNSLNP AISEDNDFNT TTNTFIDSIM AEANADNGRF MMELGKYLRV GFFPDVKTTI NLSGPEAYAA AYQDL LMFK EGSMNIHLIE ADLRNFEISK TNISQSTEQE MASLWSFDDA RAKAQFEEYK RNYFEGSLGE DDNLDFSQNI VVDKEY LLE KISSLARSSE RGYIHYIVQL QGDKISYEAA CNLFAKTPYD SVLFQKNIED SEIAYYYNPG DGEIQEIDKY KIPSIIS DR PKIKLTFIGH GKDEFNTDIF AGFDVDSLST EIEAAIDLAK EDISPKSIEI NLLGCNMFSY SINVEETYPG KLLLKVKD K ISELMPSISQ DSIIVSANQY EVRINSEGRR ELLDHSGEWI NKEESIIKDI SSKEYISFNP KENKITVKSK NLPELSTLL QEIRNNSNSS DIELEEKVML TECEINVISN IDTQIVEERI EEAKNLTSDS INYIKDEFKL IESISDALCD LKQQNELEDS HFISFEDIS ETDEGFSIRF INKETGESIF VETEKTIFSE YANHITEEIS KIKGTIFDTV NGKLVKKVNL DTTHEVNTLN A AFFIQSLI EYNSSKESLS NLSVAMKVQV YAQLFSTGLN TITDAAKVVE LVSTALDETI DLLPTLSEGL PIIATIIDGV SL GAAIKEL SETSDPLLRQ EIEAKIGIMA VNLTTATTAI ITSSLGIASG FSILLVPLAG ISAGIPSLVN NELVLRDKAT KVV DYFKHV SLVETEGVFT LLDDKIMMPQ DDLVISEIDF NNNSIVLGKC EIWRMEGGSG HTVTDDIDHF FSAPSITYRE PHLS IYDVL EVQKEELDLS KDLMVLPNAP NRVFAWETGW TPGLRSLEND GTKLLDRIRD NYEGEFYWRY FAFIADALIT TLKPR YEDT NIRINLDSNT RSFIVPIITT EYIREKLSYS FYGSGGTYAL SLSQYNMGIN IELSESDVWI IDVDNVVRDV TIESDK IKK GDLIEGILST LSIEENKIIL NSHEINFSGE VNGSNGFVSL TFSILEGINA IIEVDLLSKS YKLLISGELK ILMLNSN HI QQKIDYIGFN SELQKNIPYS FVDSEGKENG FINGSTKEGL FVSELPDVVL ISKVYMDDSK PSFGYYSNNL KDVKVITK D NVNILTGYYL KDDIKISLSL TLQDEKTIKL NSVHLDESGV AEILKFMNRK GNTNTSDSLM SFLESMNIKS IFVNFLQSN IKFILDANFI ISGTTSIGQF EFICDENDNI QPYFIKFNTL ETNYTLYVGN RQNMIVEPNY DLDDSGDISS TVINFSQKYL YGIDSCVNK VVISPNIYTD EINITPVYET NNTYPEVIVL DANYINEKIN VNINDLSIRY VWSNDGNDFI LMSTSEENKV S QVKIRFVN VFKDKTLANK LSFNFSDKQD VPVSEIILSF TPSYYEDGLI GYDLGLVSLY NEKFYINNFG MMVSGLIYIN DS LYYFKPP VNNLITGFVT VGDDKYYFNP INGGAASIGE TIIDDKNYYF NQSGVLQTGV FSTEDGFKYF APANTLDENL EGE AIDFTG KLIIDENIYY FDDNYRGAVE WKELDGEMHY FSPETGKAFK GLNQIGDYKY YFNSDGVMQK GFVSINDNKH YFDD SGVMK VGYTEIDGKH FYFAENGEMQ IGVFNTEDGF KYFAHHNEDL GNEEGEEISY SGILNFNNKI YYFDDSFTAV VGWKD LEDG SKYYFDEDTA EAYIGLSLIN DGQYYFNDDG IMQVGFVTIN DKVFYFSDSG IIESGVQNID DNYFYIDDNG IVQIGV FDT SDGYKYFAPA NTVNDNIYGQ AVEYSGLVRV GEDVYYFGET YTIETGWIYD MENESDKYYF NPETKKACKG INLIDDI KY YFDEKGIMRT GLISFENNNY YFNENGEMQF GYINIEDKMF YFGEDGVMQI GVFNTPDGFK YFAHQNTLDE NFEGESIN Y TGWLDLDEKR YYFTDEYIAA TGSVIIDGEE YYFDPDTAQL VISE

UniProtKB: Toxin B

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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 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.8 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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