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- EMDB-24260: state 4 of TcdB and FZD2 at pH5 -

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ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-24260
Titlestate 4 of TcdB and FZD2 at pH5
Map dataState 4 of TcdB and FZD2 at pH5
Sample
  • Complex: State 4 of TcdB and FZD2 at pH5
    • Protein or peptide: Toxin B
KeywordsTOXIN / HYDROLASE
Function / homology
Function and homology information


glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis ...glucosyltransferase activity / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / cysteine-type peptidase activity / host cell endosome membrane / toxin activity / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lipid binding / host cell plasma membrane / proteolysis / extracellular region / membrane / metal ion binding
Similarity search - Function
TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily ...TcdA/TcdB toxin, N-terminal helical domain / TcdB toxin N-terminal helical domain / TcdA/TcdB toxin, catalytic glycosyltransferase domain / TcdA/TcdB catalytic glycosyltransferase domain / Dermonecrotic/RTX toxin, membrane localization domain / Membrane Localization Domain / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Choline-binding repeat / Putative cell wall binding repeat / Cell wall/choline-binding repeat / Cell wall-binding repeat profile. / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Biological speciesClostridioides difficile (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.9 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-
UpdateJun 5, 2024-
Current statusJun 5, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7n9r
  • Surface level: 0.0286
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_24260.png

Downloads & links

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Map

FileDownload / File: emd_24260.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationState 4 of TcdB and FZD2 at pH5
Voxel sizeX=Y=Z: 1.06065 Å
Density
Contour LevelBy AUTHOR: 0.0286 / Movie #1: 0.0286
Minimum - Maximum-0.0016945663 - 1.8919563
Average (Standard dev.)0.00090080727 (±0.021520466)
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-0.0021.8920.001

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Supplemental data

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Sample components

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Entire : State 4 of TcdB and FZD2 at pH5

EntireName: State 4 of TcdB and FZD2 at pH5
Components
  • Complex: State 4 of TcdB and FZD2 at pH5
    • Protein or peptide: Toxin B

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Supramolecule #1: State 4 of TcdB and FZD2 at pH5

SupramoleculeName: State 4 of TcdB and FZD2 at pH5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 250 KDa

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Macromolecule #1: Toxin B

MacromoleculeName: Toxin B / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
Source (natural)Organism: Clostridioides difficile (bacteria)
Molecular weightTheoretical: 269.938438 KDa
Recombinant expressionOrganism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria)
SequenceString: MSLVNRKQLE KMANVRFRTQ EDEYVAILDA LEEYHNMSEN TVVEKYLKLK DINSLTDIYI DTYKKSGRNK ALKKFKEYLV TEVLELKNN NLTPVEKNLH FVWIGGQIND TAINYINQWK DVNSDYNVNV FYDSNAFLIN TLKKTVVESA INDTLESFRE N LNDPRFDY ...String:
MSLVNRKQLE KMANVRFRTQ EDEYVAILDA LEEYHNMSEN TVVEKYLKLK DINSLTDIYI DTYKKSGRNK ALKKFKEYLV TEVLELKNN NLTPVEKNLH FVWIGGQIND TAINYINQWK DVNSDYNVNV FYDSNAFLIN TLKKTVVESA INDTLESFRE N LNDPRFDY NKFFRKRMEI IYDKQKNFIN YYKAQREENP ELIIDDIVKT YLSNEYSKEI DELNTYIEES LNKITQNSGN DV RNFEEFK NGESFNLYEQ ELVERWNLAA ASDILRISAL KEIGGMYLDV DMLPGIQPDL FESIEKPSSV TVDFWEMTKL EAI MKYKEY IPEYTSEHFD MLDEEVQSSF ESVLASKSDK SEIFSSLGDM EASPLEVKIA FNSKGIINQG LISVKDSYCS NLIV KQIEN RYKILNNSLN PAISEDNDFN TTTNTFIDSI MAEANADNGR FMMELGKYLR VGFFPDVKTT INLSGPEAYA AAYQD LLMF KEGSMNIHLI EADLRNFEIS KTNISQSTEQ EMASLWSFDD ARAKAQFEEY KRNYFEGSLG EDDNLDFSQN IVVDKE YLL EKISSLARSS ERGYIHYIVQ LQGDKISYEA ACNLFAKTPY DSVLFQKNIE DSEIAYYYNP GDGEIQEIDK YKIPSII SD RPKIKLTFIG HGKDEFNTDI FAGFDVDSLS TEIEAAIDLA KEDISPKSIE INLLGCNMFS YSINVEETYP GKLLLKVK D KISELMPSIS QDSIIVSANQ YEVRINSEGR RELLDHSGEW INKEESIIKD ISSKEYISFN PKENKITVKS KNLPELSTL LQEIRNNSNS SDIELEEKVM LTECEINVIS NIDTQIVEER IEEAKNLTSD SINYIKDEFK LIESISDALC DLKQQNELED SHFISFEDI SETDEGFSIR FINKETGESI FVETEKTIFS EYANHITEEI SKIKGTIFDT VNGKLVKKVN LDTTHEVNTL N AAFFIQSL IEYNSSKESL SNLSVAMKVQ VYAQLFSTGL NTITDAAKVV ELVSTALDET IDLLPTLSEG LPIIATIIDG VS LGAAIKE LSETSDPLLR QEIEAKIGIM AVNLTTATTA IITSSLGIAS GFSILLVPLA GISAGIPSLV NNELVLRDKA TKV VDYFKH VSLVETEGVF TLLDDKIMMP QDDLVISEID FNNNSIVLGK CEIWRMEGGS GHTVTDDIDH FFSAPSITYR EPHL SIYDV LEVQKEELDL SKDLMVLPNA PNRVFAWETG WTPGLRSLEN DGTKLLDRIR DNYEGEFYWR YFAFIADALI TTLKP RYED TNIRINLDSN TRSFIVPIIT TEYIREKLSY SFYGSGGTYA LSLSQYNMGI NIELSESDVW IIDVDNVVRD VTIESD KIK KGDLIEGILS TLSIEENKII LNSHEINFSG EVNGSNGFVS LTFSILEGIN AIIEVDLLSK SYKLLISGEL KILMLNS NH IQQKIDYIGF NSELQKNIPY SFVDSEGKEN GFINGSTKEG LFVSELPDVV LISKVYMDDS KPSFGYYSNN LKDVKVIT K DNVNILTGYY LKDDIKISLS LTLQDEKTIK LNSVHLDESG VAEILKFMNR KGNTNTSDSL MSFLESMNIK SIFVNFLQS NIKFILDANF IISGTTSIGQ FEFICDENDN IQPYFIKFNT LETNYTLYVG NRQNMIVEPN YDLDDSGDIS STVINFSQKY LYGIDSCVN KVVISPNIYT DEINITPVYE TNNTYPEVIV LDANYINEKI NVNINDLSIR YVWSNDGNDF ILMSTSEENK V SQVKIRFV NVFKDKTLAN KLSFNFSDKQ DVPVSEIILS FTPSYYEDGL IGYDLGLVSL YNEKFYINNF GMMVSGLIYI ND SLYYFKP PVNNLITGFV TVGDDKYYFN PINGGAASIG ETIIDDKNYY FNQSGVLQTG VFSTEDGFKY FAPANTLDEN LEG EAIDFT GKLIIDENIY YFDDNYRGAV EWKELDGEMH YFSPETGKAF KGLNQIGDYK YYFNSDGVMQ KGFVSINDNK HYFD DSGVM KVGYTEIDGK HFYFAENGEM QIGVFNTEDG FKYFAHHNED LGNEEGEEIS YSGILNFNNK IYYFDDSFTA VVGWK DLED GSKYYFDEDT AEAYIGLSLI NDGQYYFNDD GIMQVGFVTI NDKVFYFSDS GIIESGVQNI DDNYFYIDDN GIVQIG VFD TSDGYKYFAP ANTVNDNIYG QAVEYSGLVR VGEDVYYFGE TYTIETGWIY DMENESDKYY FNPETKKACK GINLIDD IK YYFDEKGIMR TGLISFENNN YYFNENGEMQ FGYINIEDKM FYFGEDGVMQ IGVFNTPDGF KYFAHQNTLD ENFEGESI N YTGWLDLDEK RYYFTDEYIA ATGSVIIDGE EYYFDPDTAQ LVISE

UniProtKB: Toxin B

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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: 5
VitrificationCryogen name: ETHANE

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Electron microscopy

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

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Image processing

Startup modelType of model: OTHER / Details: model prediction
Final reconstructionResolution.type: BY AUTHOR / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 73441
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: ANGULAR RECONSTITUTION

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