+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24251 | |||||||||
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Title | State 2 of TcdB and FZD2 at pH5 | |||||||||
Map data | State 2 of TcdB and FZD2 at pH5 | |||||||||
Sample |
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Keywords | TOXIN / TOXIN-Developmental Protein complex | |||||||||
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: 5.1 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 the 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_24251.map.gz | 260.9 MB | EMDB map data format | |
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Header (meta data) | emd-24251-v30.xml emd-24251.xml | 12.8 KB 12.8 KB | Display Display | EMDB header |
Images | emd_24251.png | 58.5 KB | ||
Filedesc metadata | emd-24251.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24251 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24251 | HTTPS FTP |
-Validation report
Summary document | emd_24251_validation.pdf.gz | 338.1 KB | Display | EMDB validaton report |
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Full document | emd_24251_full_validation.pdf.gz | 337.6 KB | Display | |
Data in XML | emd_24251_validation.xml.gz | 7.3 KB | Display | |
Data in CIF | emd_24251_validation.cif.gz | 8.4 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24251 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24251 | HTTPS FTP |
-Related structure data
Related structure data | 7n97MC 7n8xC 7n95C 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_24251.map.gz / Format: CCP4 / Size: 299.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | State 2 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 2 of TcdB and FZD2 at pH5
Entire | Name: State 2 of TcdB and FZD2 at pH5 |
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Components |
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-Supramolecule #1: State 2 of TcdB and FZD2 at pH5
Supramolecule | Name: State 2 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 the frizzled 2 CRD domain
Supramolecule | Name: Ternary structure of the 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: 269.807219 KDa |
Recombinant expression | Organism: Bacillus megaterium NBRC 15308 = ATCC 14581 (bacteria) |
Sequence | String: 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 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: 5.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 75923 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |