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Open data
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Basic information
Entry | Database: PDB / ID: 7n95 | ||||||
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Title | state 1 of TcdB and FZD2 at pH5 | ||||||
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![]() | TOXIN | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å | ||||||
![]() | Jiang, M. / Zhang, J. | ||||||
Funding support | ![]()
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![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 296.5 KB | Display | ![]() |
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PDB format | ![]() | 155.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 584.8 KB | Display | ![]() |
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Full document | ![]() | 585 KB | Display | |
Data in XML | ![]() | 50.8 KB | Display | |
Data in CIF | ![]() | 84.7 KB | Display | |
Arichive directory | ![]() ![]() | 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 ( |
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Similar structure data |
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Links
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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.) ![]() ![]() |
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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.) ![]() Production host: ![]() 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 |
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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 |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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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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