+Open data
-Basic information
Entry | Database: PDB / ID: 7n8x | |||||||||
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Title | Partial C. difficile TcdB and CSPG4 fragment | |||||||||
Components |
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Keywords | TOXIN/Developmental Protein / TOXIN / TOXIN-Developmental Protein complex | |||||||||
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 / angiogenesis / collagen-containing extracellular matrix / toxin activity / 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 | |||||||||
Biological species | Homo sapiens (human) Clostridioides difficile (bacteria) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||
Authors | Jiang, M. / Zhang, J. | |||||||||
Funding support | United States, 2items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7n8x.cif.gz | 172 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n8x.ent.gz | 129 KB | Display | PDB format |
PDBx/mmJSON format | 7n8x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n8x_validation.pdf.gz | 668.3 KB | Display | wwPDB validaton report |
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Full document | 7n8x_full_validation.pdf.gz | 676.7 KB | Display | |
Data in XML | 7n8x_validation.xml.gz | 29.1 KB | Display | |
Data in CIF | 7n8x_validation.cif.gz | 42.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n8/7n8x ftp://data.pdbj.org/pub/pdb/validation_reports/n8/7n8x | HTTPS FTP |
-Related structure data
Related structure data | 24248MC 7n95C 7n97C 7n9qC 7n9rC 7n9sC 7n9yC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | 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 |
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#2: Protein | 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 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight |
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Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.5 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.19.2_4158: / Classification: refinement | ||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 470301 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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