+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24250 | |||||||||
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Title | State 1 of TcdB and FZD2 at pH5 | |||||||||
Map data | State 1 of TcdB and FZD2 at pH5 | |||||||||
Sample |
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Keywords | TOXIN | |||||||||
Function / homology | Function and homology information muscular septum morphogenesis / : / cochlea morphogenesis / membranous septum morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / non-canonical Wnt signaling pathway / inner ear receptor cell development / glucosyltransferase activity ...muscular septum morphogenesis / : / cochlea morphogenesis / membranous septum morphogenesis / WNT5A-dependent internalization of FZD2, FZD5 and ROR2 / hard palate development / Wnt receptor activity / 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 / positive regulation of DNA-binding transcription factor activity / clathrin-coated endocytic vesicle membrane / neuron differentiation / sensory perception of smell / Wnt signaling pathway / cell-cell signaling / 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 | Clostridioides difficile (bacteria) / Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.1 Å | |||||||||
Authors | Jiang M / Zhang J | |||||||||
Funding support | United States, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_24250.map.gz | 266.4 MB | EMDB map data format | |
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Header (meta data) | emd-24250-v30.xml emd-24250.xml | 12.7 KB 12.7 KB | Display Display | EMDB header |
Images | emd_24250.png | 66.8 KB | ||
Filedesc metadata | emd-24250.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24250 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24250 | HTTPS FTP |
-Validation report
Summary document | emd_24250_validation.pdf.gz | 319.2 KB | Display | EMDB validaton report |
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Full document | emd_24250_full_validation.pdf.gz | 318.7 KB | Display | |
Data in XML | emd_24250_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_24250_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24250 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24250 | HTTPS FTP |
-Related structure data
Related structure data | 7n95MC 7n8xC 7n97C 7n9qC 7n9rC 7n9sC 7n9yC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_24250.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | State 1 of TcdB and FZD2 at pH5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.06065 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : State 1 of TcdB and FZD2 at pH5
Entire | Name: State 1 of TcdB and FZD2 at pH5 |
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Components |
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-Supramolecule #1: State 1 of TcdB and FZD2 at pH5
Supramolecule | Name: State 1 of TcdB and FZD2 at pH5 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
Molecular weight | Theoretical: 250 KDa |
-Supramolecule #2: Ternary structure of frizzled-2 CRD domain
Supramolecule | Name: Ternary structure of frizzled-2 CRD domain / type: organelle_or_cellular_component / ID: 2 / Parent: 1 / Macromolecule list: #1 |
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Source (natural) | Organism: Homo sapiens (human) |
-Supramolecule #3: Ternary structure of Clostridium difficile TcdB
Supramolecule | Name: Ternary structure of Clostridium difficile TcdB / type: organelle_or_cellular_component / ID: 3 / Parent: 1 / Macromolecule list: #2 |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
-Macromolecule #1: Frizzled-2
Macromolecule | Name: Frizzled-2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Homo sapiens (human) |
Molecular weight | Theoretical: 13.834912 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: DHGFCQPISI PLCTDIAYNQ TIMPNLLGHT NQEDAGLEVH QFYPLVKVQC SPELRFFLCS MYAPVCTVLE QAIPPCRSIC ERARQGCEA LMNKFGFQWP ERLRCEHFPR HGAEQICVGQ NH UniProtKB: Frizzled-2 |
-Macromolecule #2: Toxin B
Macromolecule | Name: Toxin B / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO EC number: Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases |
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Source (natural) | Organism: Clostridioides difficile (bacteria) |
Molecular weight | Theoretical: 269.938438 KDa |
Recombinant expression | Organism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER / Details: model prediction |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 101248 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |