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- PDB-6c0b: Structural basis for recognition of frizzled proteins by Clostrid... -

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Basic information

Entry
Database: PDB / ID: 6c0b
TitleStructural basis for recognition of frizzled proteins by Clostridium difficile toxin B
Components
  • Frizzled-2
  • Toxin B
KeywordsTOXIN / complex
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 / glycosyltransferase activity / 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 / peptidase activity / 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 / Frizzled cysteine-rich domain / Frizzled 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 ...Frizzled 2, cysteine-rich domain / Frizzled cysteine-rich domain / Frizzled 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
MALONATE ION / PALMITOLEIC ACID / Glycosylating toxin TcdB / Toxin B / Frizzled-2
Similarity search - Component
Biological speciesClostridioides difficile (bacteria)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsChen, P. / Lam, K. / Jin, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R01AI091823, R01 AI125704, and R21AI123920 United States
CitationJournal: Science / Year: 2018
Title: Structural basis for recognition of frizzled proteins byClostridium difficiletoxin B.
Authors: Chen, P. / Tao, L. / Wang, T. / Zhang, J. / He, A. / Lam, K.H. / Liu, Z. / He, X. / Perry, K. / Dong, M. / Jin, R.
History
DepositionDec 28, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 16, 2018Provider: repository / Type: Initial release
Revision 1.1May 23, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Feb 20, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Dec 18, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toxin B
B: Frizzled-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,2537
Polymers76,4712
Non-polymers7825
Water66737
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Frizzled-2
hetero molecules

B: Frizzled-2
hetero molecules

A: Toxin B
hetero molecules

A: Toxin B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)154,50514
Polymers152,9424
Non-polymers1,56410
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_576x,-y+2,-z+11
crystal symmetry operation5_555x+1/2,y+1/2,z1
crystal symmetry operation8_566x+1/2,-y+3/2,-z+11
Buried area8370 Å2
ΔGint-23 kcal/mol
Surface area57650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.611, 175.613, 174.423
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Toxin B


Mass: 59023.160 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridioides difficile (bacteria) / Gene: tcdB / Production host: Escherichia coli (E. coli) / References: UniProt: M4NKV9, UniProt: P18177*PLUS
#2: Protein Frizzled-2 / / hFz2 / FzE2


Mass: 17447.770 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FZD2 / Production host: Mammalia (mammals) / References: UniProt: Q14332

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Sugars , 1 types, 1 molecules

#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 3 types, 41 molecules

#3: Chemical ChemComp-MLI / MALONATE ION / Malonic acid


Mass: 102.046 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H2O4
#5: Chemical ChemComp-PAM / PALMITOLEIC ACID / Palmitoleic acid


Mass: 254.408 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H30O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.02 Å3/Da / Density % sol: 69.4 %
Crystal growTemperature: 292.15 K / Method: vapor diffusion, hanging drop
Details: 0.1 M sodium acetate (pH 5.0) and 1 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 10, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→87.86 Å / Num. obs: 39399 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.0468 / Net I/σ(I): 18.25
Reflection shellResolution: 2.5→2.56 Å / Rmerge(I) obs: 0.595 / Num. unique obs: 3920

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→87.806 Å / SU ML: 0.36 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 32.91
RfactorNum. reflection% reflection
Rfree0.2374 1960 4.98 %
Rwork0.1987 --
obs0.2006 39325 98.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→87.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4978 0 53 37 5068
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085127
X-RAY DIFFRACTIONf_angle_d1.0176944
X-RAY DIFFRACTIONf_dihedral_angle_d16.9423092
X-RAY DIFFRACTIONf_chiral_restr0.06794
X-RAY DIFFRACTIONf_plane_restr0.006895
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.46881400.39522646X-RAY DIFFRACTION99
2.5625-2.63180.37311370.35132643X-RAY DIFFRACTION99
2.6318-2.70930.34131360.31412657X-RAY DIFFRACTION99
2.7093-2.79670.36061260.29542678X-RAY DIFFRACTION99
2.7967-2.89670.33911510.29232661X-RAY DIFFRACTION99
2.8967-3.01270.33821420.28912637X-RAY DIFFRACTION98
3.0127-3.14980.28431510.25332623X-RAY DIFFRACTION98
3.1498-3.31580.31931230.23672679X-RAY DIFFRACTION98
3.3158-3.52360.27691320.21482674X-RAY DIFFRACTION98
3.5236-3.79570.21551450.19722667X-RAY DIFFRACTION98
3.7957-4.17760.2191560.16912662X-RAY DIFFRACTION98
4.1776-4.78210.15961420.13122676X-RAY DIFFRACTION98
4.7821-6.02480.1881480.14972694X-RAY DIFFRACTION98
6.0248-87.86070.19261310.17072768X-RAY DIFFRACTION95

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