+Open data
-Basic information
Entry | Database: PDB / ID: 7n95 | ||||||
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Title | state 1 of TcdB and FZD2 at pH5 | ||||||
Components |
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Keywords | TOXIN | ||||||
Function / homology | Function and homology information muscular septum morphogenesis / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / hard palate development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / non-canonical Wnt signaling pathway / membranous septum morphogenesis / Wnt receptor activity / inner ear receptor cell development / glucosyltransferase activity ...muscular septum morphogenesis / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / hard palate development / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / non-canonical Wnt signaling pathway / membranous septum morphogenesis / Wnt receptor activity / inner ear receptor cell development / glucosyltransferase activity / endothelial cell differentiation / Wnt-protein binding / Class B/2 (Secretin family receptors) / Disassembly of the destruction complex and recruitment of AXIN to the membrane / Wnt signaling pathway, planar cell polarity pathway / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / outflow tract morphogenesis / canonical Wnt signaling pathway / cysteine-type peptidase activity / host cell endosome membrane / Asymmetric localization of PCP proteins / TCF dependent signaling in response to WNT / PDZ domain binding / G protein-coupled receptor activity / clathrin-coated endocytic vesicle membrane / neuron differentiation / Wnt signaling pathway / positive regulation of DNA-binding transcription factor activity / sensory perception of smell / Ca2+ pathway / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / focal adhesion / lipid binding / host cell plasma membrane / positive regulation of DNA-templated transcription / proteolysis / extracellular region / membrane / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Clostridioides difficile (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 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 | 7n95.cif.gz | 296.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7n95.ent.gz | 155.7 KB | Display | PDB format |
PDBx/mmJSON format | 7n95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7n95_validation.pdf.gz | 584.8 KB | Display | wwPDB validaton report |
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Full document | 7n95_full_validation.pdf.gz | 585 KB | Display | |
Data in XML | 7n95_validation.xml.gz | 50.8 KB | Display | |
Data in CIF | 7n95_validation.cif.gz | 84.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n9/7n95 ftp://data.pdbj.org/pub/pdb/validation_reports/n9/7n95 | HTTPS FTP |
-Related structure data
Related structure data | 24250MC 7n8xC 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: 13834.912 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FZD2 / Production host: Homo sapiens (human) / References: UniProt: Q14332 |
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#2: 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 |
-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: 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: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101248 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
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