+Open data
-Basic information
Entry | Database: PDB / ID: 7n9r | ||||||
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Title | state 4 of TcdB and FZD2 at pH5 | ||||||
Components | Toxin B | ||||||
Keywords | HYDROLASE / TOXIN | ||||||
Function / homology | Function and homology information glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / 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 / membrane / metal ion binding Similarity search - Function | ||||||
Biological species | Clostridioides difficile (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.9 Å | ||||||
Authors | Jiang, M. / Zhang, J. | ||||||
Funding support | United States, 1items
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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 | 7n9r.cif.gz | 281.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n9r.ent.gz | 148.9 KB | Display | PDB format |
PDBx/mmJSON format | 7n9r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n9r_validation.pdf.gz | 579.9 KB | Display | wwPDB validaton report |
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Full document | 7n9r_full_validation.pdf.gz | 580.1 KB | Display | |
Data in XML | 7n9r_validation.xml.gz | 48.4 KB | Display | |
Data in CIF | 7n9r_validation.cif.gz | 80.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/7n9r ftp://data.pdbj.org/pub/pdb/validation_reports/n9/7n9r | HTTPS FTP |
-Related structure data
Related structure data | 24260MC 7n8xC 7n95C 7n97C 7n9qC 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: 269938.438 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 |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: State 4 of TcdB and FZD2 at pH5 / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Value: 0.25 MDa / Experimental value: YES |
Source (natural) | Organism: Clostridioides difficile (bacteria) |
Source (recombinant) | Organism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria) |
Buffer solution | pH: 5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
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 K3 (6k 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: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 73441 / Symmetry type: POINT | ||||||||||||||||||||||||
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