+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-24264 | |||||||||
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Title | Full-length TcdB and CSPG4 (401-560) complex | |||||||||
Map data | Full-length TcdB and CSPG4 (401-560) complex | |||||||||
Sample |
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Keywords | TOXIN / SIGNALING PROTEIN-Hydrolase complex | |||||||||
Function / homology | Function and homology information Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / substrate-dependent cell migration ...Chondroitin sulfate biosynthesis / Defective CHST3 causes SEDCJD / Defective CHST14 causes EDS, musculocontractural type / Defective CHSY1 causes TPBS / Dermatan sulfate biosynthesis / Defective B3GALT6 causes EDSP2 and SEMDJL1 / CS/DS degradation / Defective B4GALT7 causes EDS, progeroid type / Defective B3GAT3 causes JDSSDHD / substrate-dependent cell migration / A tetrasaccharide linker sequence is required for GAG synthesis / glial cell migration / tissue remodeling / ruffle assembly / glucosyltransferase activity / Differentiation of keratinocytes in interfollicular epidermis in mammalian skin / host cell cytosol / Transferases; Glycosyltransferases; Hexosyltransferases / lamellipodium membrane / platelet-derived growth factor receptor signaling pathway / coreceptor activity / cysteine-type peptidase activity / ruffle / lysosomal lumen / host cell endosome membrane / Golgi lumen / positive regulation of peptidyl-tyrosine phosphorylation / angiogenesis / collagen-containing extracellular matrix / toxin activity / positive regulation of MAPK cascade / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / intracellular signal transduction / apical plasma membrane / focal adhesion / lipid binding / protein kinase binding / host cell plasma membrane / cell surface / proteolysis / extracellular exosome / extracellular region / nucleoplasm / membrane / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Clostridioides difficile (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.8 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_24264.map.gz | 37.5 MB | EMDB map data format | |
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Header (meta data) | emd-24264-v30.xml emd-24264.xml | 12.5 KB 12.5 KB | Display Display | EMDB header |
Images | emd_24264.png | 57.6 KB | ||
Filedesc metadata | emd-24264.cif.gz | 6.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-24264 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-24264 | HTTPS FTP |
-Validation report
Summary document | emd_24264_validation.pdf.gz | 323 KB | Display | EMDB validaton report |
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Full document | emd_24264_full_validation.pdf.gz | 322.5 KB | Display | |
Data in XML | emd_24264_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | emd_24264_validation.cif.gz | 8.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24264 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-24264 | HTTPS FTP |
-Related structure data
Related structure data | 7n9yMC 7n8xC 7n95C 7n97C 7n9qC 7n9rC 7n9sC 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_24264.map.gz / Format: CCP4 / Size: 247.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Full-length TcdB and CSPG4 (401-560) complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.13 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 : Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
Entire | Name: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560) |
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Components |
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-Supramolecule #1: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560)
Supramolecule | Name: Ternary complex of Clostridium difficile TcdB and CSPG4 (401-560) type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Supramolecule #2: Ternary structure of CSPG4 (401-560)
Supramolecule | Name: Ternary structure of CSPG4 (401-560) / 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: Chondroitin sulfate proteoglycan 4
Macromolecule | Name: Chondroitin sulfate proteoglycan 4 / 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: 15.565927 KDa |
Recombinant expression | Organism: Homo sapiens (human) |
Sequence | String: LPEPCVPEPG LPPVFANFTQ LLTISPLVVA EGGTAWLEWR HVQPTLDLME AELRKSQVLF SVTRGARHGE LELDIPGAQA RKMFTLLDV VNRKARFIHD GSEDTSDQLV LEVSVTARVP MPSCLRRGQT YLLPIQVNPV N UniProtKB: Chondroitin sulfate proteoglycan 4 |
-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: Priestia 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: 7.5 |
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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 K2 SUMMIT (4k 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: EMDB MAP |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 470301 |
Initial angle assignment | Type: RANDOM ASSIGNMENT |
Final angle assignment | Type: ANGULAR RECONSTITUTION |