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

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Basic information

Entry
Database: PDB / ID: 7n8x
TitlePartial C. difficile TcdB and CSPG4 fragment
Components
  • Chondroitin sulfate proteoglycan 4
  • Toxin B
KeywordsTOXIN/Developmental Protein / TOXIN / TOXIN-Developmental Protein 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. / MARTX cysteine protease (CPD) 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 ...CSPG repeat / : / Cadherin-like / CSPG repeat profile. / MARTX cysteine protease (CPD) 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. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toxin B / Chondroitin sulfate proteoglycan 4
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsJiang, M. / Zhang, J.
Funding support United States, 2items
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, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 2, 2022Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_admin / em_entity_assembly_molwt / pdbx_entry_details / pdbx_modification_feature
Item: _em_admin.last_update / _em_entity_assembly_molwt.id
Revision 1.2May 14, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1May 14, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

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  • Deposited structure unit
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Structure viewerMolecule:
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Assembly

Deposited unit
B: Chondroitin sulfate proteoglycan 4
A: Toxin B


Theoretical massNumber of molelcules
Total (without water)185,0452
Polymers185,0452
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein Chondroitin sulfate proteoglycan 4 / Chondroitin sulfate proteoglycan NG2 / Melanoma chondroitin sulfate proteoglycan / Melanoma- ...Chondroitin sulfate proteoglycan NG2 / Melanoma chondroitin sulfate proteoglycan / Melanoma-associated chondroitin sulfate proteoglycan


Mass: 15565.927 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CSPG4, MCSP / Production host: Homo sapiens (human) / References: UniProt: Q6UVK1
#2: Protein Toxin B


Mass: 169479.141 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB, toxB
Production host: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
References: UniProt: P18177, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1The complex of TcdB and CSPG4 fragmentCOMPLEXall0RECOMBINANT
2Ternary structure of C-terminus of CSPG4 domain 1ORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3Ternary structure of Clostridium difficile TcdBORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.25 MDaYES
22
33
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Clostridioides difficile (bacteria)1496
32Homo sapiens (human)9606
43Clostridioides difficile (bacteria)1496
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)1348623
32Homo sapiens (human)9606
43Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)1348623
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470301 / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0036741
ELECTRON MICROSCOPYf_angle_d0.699138
ELECTRON MICROSCOPYf_dihedral_angle_d6.191894
ELECTRON MICROSCOPYf_chiral_restr0.0491031
ELECTRON MICROSCOPYf_plane_restr0.0061193

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