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- EMDB-24261: TcdB and frizzled-2 CRD complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24261
TitleTcdB and frizzled-2 CRD complex
Map dataTcdB and frizzled-2 CRD complex
Sample
  • Complex: TcdB and frizzled-2 CRD complex at pH7.5
    • Organelle or cellular component: Ternary structure of state 4 Clostridium difficile TcdB
      • Protein or peptide: Toxin B
    • Organelle or cellular component: frizzled-2 CRD
      • Protein or peptide: Frizzled-2
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 speciesClostridioides difficile (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.1 Å
AuthorsJiang M / Zhang J
Funding support United States, 1 items
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 18, 2021-
Header (metadata) releaseMar 2, 2022-
Map releaseMar 2, 2022-
UpdateMar 2, 2022-
Current statusMar 2, 2022Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7n9s
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24261.png

Downloads & links

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Map

FileDownload / File: emd_24261.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationTcdB and frizzled-2 CRD complex
Voxel sizeX=Y=Z: 1.06065 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.03531619 - 0.09741848
Average (Standard dev.)0.000110527944 (±0.0017976629)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions428428428
Spacing428428428
CellA=B=C: 453.9582 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.06064953271031.06064953271031.0606495327103
M x/y/z428428428
origin x/y/z0.0000.0000.000
length x/y/z453.958453.958453.958
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS428428428
D min/max/mean-0.0350.0970.000

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Supplemental data

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Sample components

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Entire : TcdB and frizzled-2 CRD complex at pH7.5

EntireName: TcdB and frizzled-2 CRD complex at pH7.5
Components
  • Complex: TcdB and frizzled-2 CRD complex at pH7.5
    • Organelle or cellular component: Ternary structure of state 4 Clostridium difficile TcdB
      • Protein or peptide: Toxin B
    • Organelle or cellular component: frizzled-2 CRD
      • Protein or peptide: Frizzled-2

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Supramolecule #1: TcdB and frizzled-2 CRD complex at pH7.5

SupramoleculeName: TcdB and frizzled-2 CRD complex at pH7.5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
Molecular weightExperimental: 250 KDa

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Supramolecule #2: Ternary structure of state 4 Clostridium difficile TcdB

SupramoleculeName: Ternary structure of state 4 Clostridium difficile TcdB
type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #2

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Supramolecule #3: frizzled-2 CRD

SupramoleculeName: frizzled-2 CRD / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Clostridioides difficile (bacteria)
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)

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Macromolecule #1: Frizzled-2

MacromoleculeName: Frizzled-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.834912 KDa
Recombinant expressionOrganism: Homo sapiens (human)
SequenceString:
DHGFCQPISI PLCTDIAYNQ TIMPNLLGHT NQEDAGLEVH QFYPLVKVQC SPELRFFLCS MYAPVCTVLE QAIPPCRSIC ERARQGCEA LMNKFGFQWP ERLRCEHFPR HGAEQICVGQ NH

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Macromolecule #2: Toxin B

MacromoleculeName: Toxin B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 269.807219 KDa
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
SequenceString: SLVNRKQLEK MANVRFRTQE DEYVAILDAL EEYHNMSENT VVEKYLKLKD INSLTDIYID TYKKSGRNKA LKKFKEYLVT EVLELKNNN LTPVEKNLHF VWIGGQINDT AINYINQWKD VNSDYNVNVF YDSNAFLINT LKKTVVESAI NDTLESFREN L NDPRFDYN ...String:
SLVNRKQLEK MANVRFRTQE DEYVAILDAL EEYHNMSENT VVEKYLKLKD INSLTDIYID TYKKSGRNKA LKKFKEYLVT EVLELKNNN LTPVEKNLHF VWIGGQINDT AINYINQWKD VNSDYNVNVF YDSNAFLINT LKKTVVESAI NDTLESFREN L NDPRFDYN KFFRKRMEII YDKQKNFINY YKAQREENPE LIIDDIVKTY LSNEYSKEID ELNTYIEESL NKITQNSGND VR NFEEFKN GESFNLYEQE LVERWNLAAA SDILRISALK EIGGMYLDVD MLPGIQPDLF ESIEKPSSVT VDFWEMTKLE AIM KYKEYI PEYTSEHFDM LDEEVQSSFE SVLASKSDKS EIFSSLGDME ASPLEVKIAF NSKGIINQGL ISVKDSYCSN LIVK QIENR YKILNNSLNP AISEDNDFNT TTNTFIDSIM AEANADNGRF MMELGKYLRV GFFPDVKTTI NLSGPEAYAA AYQDL LMFK EGSMNIHLIE ADLRNFEISK TNISQSTEQE MASLWSFDDA RAKAQFEEYK RNYFEGSLGE DDNLDFSQNI VVDKEY LLE KISSLARSSE RGYIHYIVQL QGDKISYEAA CNLFAKTPYD SVLFQKNIED SEIAYYYNPG DGEIQEIDKY KIPSIIS DR PKIKLTFIGH GKDEFNTDIF AGFDVDSLST EIEAAIDLAK EDISPKSIEI NLLGCNMFSY SINVEETYPG KLLLKVKD K ISELMPSISQ DSIIVSANQY EVRINSEGRR ELLDHSGEWI NKEESIIKDI SSKEYISFNP KENKITVKSK NLPELSTLL QEIRNNSNSS DIELEEKVML TECEINVISN IDTQIVEERI EEAKNLTSDS INYIKDEFKL IESISDALCD LKQQNELEDS HFISFEDIS ETDEGFSIRF INKETGESIF VETEKTIFSE YANHITEEIS KIKGTIFDTV NGKLVKKVNL DTTHEVNTLN A AFFIQSLI EYNSSKESLS NLSVAMKVQV YAQLFSTGLN TITDAAKVVE LVSTALDETI DLLPTLSEGL PIIATIIDGV SL GAAIKEL SETSDPLLRQ EIEAKIGIMA VNLTTATTAI ITSSLGIASG FSILLVPLAG ISAGIPSLVN NELVLRDKAT KVV DYFKHV SLVETEGVFT LLDDKIMMPQ DDLVISEIDF NNNSIVLGKC EIWRMEGGSG HTVTDDIDHF FSAPSITYRE PHLS IYDVL EVQKEELDLS KDLMVLPNAP NRVFAWETGW TPGLRSLEND GTKLLDRIRD NYEGEFYWRY FAFIADALIT TLKPR YEDT NIRINLDSNT RSFIVPIITT EYIREKLSYS FYGSGGTYAL SLSQYNMGIN IELSESDVWI IDVDNVVRDV TIESDK IKK GDLIEGILST LSIEENKIIL NSHEINFSGE VNGSNGFVSL TFSILEGINA IIEVDLLSKS YKLLISGELK ILMLNSN HI QQKIDYIGFN SELQKNIPYS FVDSEGKENG FINGSTKEGL FVSELPDVVL ISKVYMDDSK PSFGYYSNNL KDVKVITK D NVNILTGYYL KDDIKISLSL TLQDEKTIKL NSVHLDESGV AEILKFMNRK GNTNTSDSLM SFLESMNIKS IFVNFLQSN IKFILDANFI ISGTTSIGQF EFICDENDNI QPYFIKFNTL ETNYTLYVGN RQNMIVEPNY DLDDSGDISS TVINFSQKYL YGIDSCVNK VVISPNIYTD EINITPVYET NNTYPEVIVL DANYINEKIN VNINDLSIRY VWSNDGNDFI LMSTSEENKV S QVKIRFVN VFKDKTLANK LSFNFSDKQD VPVSEIILSF TPSYYEDGLI GYDLGLVSLY NEKFYINNFG MMVSGLIYIN DS LYYFKPP VNNLITGFVT VGDDKYYFNP INGGAASIGE TIIDDKNYYF NQSGVLQTGV FSTEDGFKYF APANTLDENL EGE AIDFTG KLIIDENIYY FDDNYRGAVE WKELDGEMHY FSPETGKAFK GLNQIGDYKY YFNSDGVMQK GFVSINDNKH YFDD SGVMK VGYTEIDGKH FYFAENGEMQ IGVFNTEDGF KYFAHHNEDL GNEEGEEISY SGILNFNNKI YYFDDSFTAV VGWKD LEDG SKYYFDEDTA EAYIGLSLIN DGQYYFNDDG IMQVGFVTIN DKVFYFSDSG IIESGVQNID DNYFYIDDNG IVQIGV FDT SDGYKYFAPA NTVNDNIYGQ AVEYSGLVRV GEDVYYFGET YTIETGWIYD MENESDKYYF NPETKKACKG INLIDDI KY YFDEKGIMRT GLISFENNNY YFNENGEMQF GYINIEDKMF YFGEDGVMQI GVFNTPDGFK YFAHQNTLDE NFEGESIN Y TGWLDLDEKR YYFTDEYIAA TGSVIIDGEE YYFDPDTAQL VISE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: OTHER / Details: model prediction
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 81240

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