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- PDB-7n95: state 1 of TcdB and FZD2 at pH5 -

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Basic information

Entry
Database: PDB / ID: 7n95
Titlestate 1 of TcdB and FZD2 at pH5
Components
  • Frizzled-2
  • Toxin B
KeywordsTOXIN
Function / homology
Function and homology information


muscular septum morphogenesis / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / membranous septum morphogenesis / non-canonical Wnt signaling pathway / inner ear receptor cell development / glucosyltransferase activity ...muscular septum morphogenesis / planar cell polarity pathway involved in neural tube closure / cochlea morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / membranous septum morphogenesis / non-canonical Wnt signaling pathway / inner ear receptor cell development / glucosyltransferase activity / Wnt-protein binding / endothelial cell differentiation / 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 / G protein-coupled receptor activity / PDZ domain binding / 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
Frizzled 2, cysteine-rich domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Frizzled/Smoothened, transmembrane domain / TcdA/TcdB toxin, pore forming domain / Frizzled/Smoothened family membrane region ...Frizzled 2, cysteine-rich domain / Dermonecrotic/RTX toxin, membrane localization domain / TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / Membrane Localization Domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Frizzled/Smoothened, transmembrane domain / TcdA/TcdB toxin, pore forming domain / Frizzled/Smoothened family membrane region / TcdA/TcdB pore forming domain / Frizzled/Smoothened family membrane region / Frizzled/secreted frizzled-related protein / Frizzled / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Frizzled domain / Frizzled cysteine-rich domain superfamily / Fz domain / Frizzled (fz) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / GPCR, family 2-like / G-protein coupled receptors family 2 profile 2. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Toxin B / Frizzled-2
Similarity search - Component
Biological speciesHomo sapiens (human)
Clostridioides difficile (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.1 Å
AuthorsJiang, M. / Zhang, J.
Funding support United States, 1items
OrganizationGrant numberCountry
Welch Foundation 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

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Structure visualization

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Assembly

Deposited unit
B: Frizzled-2
A: Toxin B


Theoretical massNumber of molelcules
Total (without water)283,7732
Polymers283,7732
Non-polymers00
Water0
1


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

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Components

#1: Protein Frizzled-2 / / Fz-2 / hFz2 / FzE2


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
#2: Protein Toxin B


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

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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
1State 1 of TcdB and FZD2 at pH5COMPLEXall0RECOMBINANT
2Ternary structure of frizzled-2 CRD domainORGANELLE OR CELLULAR COMPONENT#11RECOMBINANT
3Ternary structure of Clostridium difficile TcdBORGANELLE OR CELLULAR COMPONENT#21RECOMBINANT
Molecular weight
IDEntity assembly-IDValue (°)Experimental value
110.25 MDaYES
12
13
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: 5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
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 FIELDBright-field microscopy
Image recordingElectron dose: 40 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.19.2_4158: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 101248 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00319995
ELECTRON MICROSCOPYf_angle_d0.66527065
ELECTRON MICROSCOPYf_dihedral_angle_d4.8782621
ELECTRON MICROSCOPYf_chiral_restr0.0472979
ELECTRON MICROSCOPYf_plane_restr0.0043527

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