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Yorodumi- EMDB-10796: Morganella morganii TcdA4 in complex with porcine mucosa heparin -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10796 | |||||||||
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Title | Morganella morganii TcdA4 in complex with porcine mucosa heparin | |||||||||
Map data | ||||||||||
Sample |
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Keywords | toxin / complex / glycan | |||||||||
Biological species | Morganella morganii (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.2 Å | |||||||||
Authors | Roderer D / Broecker F / Sitsel O / Kaplonek P / Leidreiter F / Seeberger PH / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Glycan-dependent cell adhesion mechanism of Tc toxins. Authors: Daniel Roderer / Felix Bröcker / Oleg Sitsel / Paulina Kaplonek / Franziska Leidreiter / Peter H Seeberger / Stefan Raunser / Abstract: Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor-toxin interaction and membrane permeation, TcB ...Toxin complex (Tc) toxins are virulence factors of pathogenic bacteria. Tcs are composed of three subunits: TcA, TcB and TcC. TcA facilitates receptor-toxin interaction and membrane permeation, TcB and TcC form a toxin-encapsulating cocoon. While the mechanisms of holotoxin assembly and pore formation have been described, little is known about receptor binding of TcAs. Here, we identify heparins/heparan sulfates and Lewis antigens as receptors for different TcAs from insect and human pathogens. Glycan array screening reveals that all tested TcAs bind negatively charged heparins. Cryo-EM structures of Morganella morganii TcdA4 and Xenorhabdus nematophila XptA1 reveal that heparins/heparan sulfates unexpectedly bind to different regions of the shell domain, including receptor-binding domains. In addition, Photorhabdus luminescens TcdA1 binds to Lewis antigens with micromolar affinity. Here, the glycan interacts with the receptor-binding domain D of the toxin. Our results suggest a glycan dependent association mechanism of Tc toxins on the host cell surface. | |||||||||
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_10796.map.gz | 11.9 MB | EMDB map data format | |
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Header (meta data) | emd-10796-v30.xml emd-10796.xml | 14 KB 14 KB | Display Display | EMDB header |
Images | emd_10796.png | 155.5 KB | ||
Filedesc metadata | emd-10796.cif.gz | 7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10796 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10796 | HTTPS FTP |
-Validation report
Summary document | emd_10796_validation.pdf.gz | 237.1 KB | Display | EMDB validaton report |
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Full document | emd_10796_full_validation.pdf.gz | 236.2 KB | Display | |
Data in XML | emd_10796_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10796 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10796 | HTTPS FTP |
-Related structure data
Related structure data | 6yewMC 6yeyC 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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-Map
File | Download / File: emd_10796.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.11 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 : Morganella morganii TcdA4 pentamer in complex with porcine mucosa...
Entire | Name: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin |
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Components |
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-Supramolecule #1: Morganella morganii TcdA4 pentamer in complex with porcine mucosa...
Supramolecule | Name: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Morganella morganii (bacteria) |
Molecular weight | Theoretical: 1.4 MDa |
-Macromolecule #1: Insecticidal toxin protein
Macromolecule | Name: Insecticidal toxin protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO |
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Source (natural) | Organism: Morganella morganii (bacteria) |
Molecular weight | Theoretical: 275.658312 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MDQITRILEK LNQQRSGETT VTLADFMPMS LAEIRSQNTG RLSREEAQLL HRAAQKEKQN NILYTARMLT RANPLLKKEM NTARYYGAT PYGYDDIIPP RAEKFVAPGA VSSMFSPAGY LTELYREARG LHPKDSDRNL DKRRQDLAKL VLSQDNLDNE I SALSLANE ...String: MDQITRILEK LNQQRSGETT VTLADFMPMS LAEIRSQNTG RLSREEAQLL HRAAQKEKQN NILYTARMLT RANPLLKKEM NTARYYGAT PYGYDDIIPP RAEKFVAPGA VSSMFSPAGY LTELYREARG LHPKDSDRNL DKRRQDLAKL VLSQDNLDNE I SALSLANE QLETALMAQT GKTDKNKYYE TLATSRRSGV TPYNAPFEGI HNALAQRNFV LPDNILSNPA KFAILAAYDA GI SPKLYNI LTEDTESLTG SDLENSLKRN FPKVKIKDLM TLDALANYYE LPADDIQALI AAEITGRLPT PDVYNDDNKL VIP AINTGG KITFSELAKT QSDEKQADYI DLIPQGGNQF LVNFSVKKTK KDATHFSIGY NKSFNNLADK NGFVPLAGEH YSIP VTLDA KILEKKTKIG ITRKKPEPAS DENHYTSATF TIHPNAEPGI WLLRLNKTLR LAKVSGMTPH ETQHALIHVR NDSSE YELR RFTETLLYRK RYGIDTETAL MLCNAGISRI SYDGQLSHFD RLFNNPPLNG VTYTLGGDDI LMEPDAGDPR REVLKR AFR VDNTGLWQLL VITNRENKSK TIENKTEKLR GLLFVRLLAD VHNLTVAQLD ALLQISPYNS MNVYALDGKT RQKMLSF LS RITQWLNTQN ITVEQLMLLL DKISPAAPTK EMQVLLDLLR NGGIDKTNTK TLYTTMAPVI TAAMQLDITE SGEALLRW L DNNHPAGILT TSEARKLIIK KGQTAGDKEK LAAWCQALAQ RVLVIRTFTL SNAELQTLSQ GAPAGTITEL YNISDFHNL INRCGEQAGT VLDALQSGTL TVKILAQALN LSEEVITQAL TLAGQKPELT TWAQLAVLPP RLDLADTLHI TPKDITTLLT VSENVRPFY TDLSALAGLL QAGLNEQQTK QLQNQSEPRR NEALSGEYRS LVMNNPVADR DDIWRNLLVD GKVSAEITTT L LADAIAGI QLYINRTIAG DEPGADSDAL ERQFFKDWDA CNKRYSTWAG VSQLVYYPEN FVDPTLRTGQ TGMMNTMLEQ LS QSELNKD TLENGFRQYL TAFEQVADLK VVSGYHDTVN INQGNTWFIG TSQTEPKKYY WRKADHSKCQ NGRFAANAWS DWK EITCAV NPYGDMVRPV IFHSRLYLLW IEKQVQKDNT GKDTASFTLK LTHVKYDGSW ASPFSYDITE KNISGWKKTG LYCA ASQED NSLLIAWYQI EKETQPNSFG LHIQPDMSCK KEPNIAGILA TVTHQLDTET TVRVNTLLNR ISSFEFTLEK QEGNK EIDL VISHGDYTVK TENSISALIL NPTAYINITP YKLFSDIPDF YREKYITHLN SHSGTVYAPE SKKMEPANNA ISDKVN ACA VYTYNNKPPK KHISLSIGKN YPLITPLELV GRKLESFFIK HKETSALYYT YGDATDDRLT LEEDKYTIST GEKKLGT LS LGKMIAQVKT ISSDDISMEI ELNSTKFETI TGSDVGLRPP LYPTVSRETL AFPFGKLSIT IPAGADINNL DCTIKVRF K NTDVLAATTT YKLVIKKTDP VQKVISLYTT PDGAQYMEWD GYRTRLNTLF TRQLIERANN GIDAILSPET QYLPEPKPG QGTYVTLILK PYDKNTHGTN RAFTIYYSND ATGSGKFPVY SGSLSVTDNT EVKLFIPLIK PGKNAVSQSA GAQQDTLYLN ATYQKEATK QILLFRTDNN PEGWTLDKSV NNGTFAGLAE NGVTGLLQSG EPMDFSGANA LYFWELFYYT PMMVATRLLQ E QNFTEANR WLSYIWQPAA SGAGDWRVRP LKEDTSWNAD PLDSVDPDAV AQNDPMHYKV STLMKLLDLL IARGDKAYRM QE RDTLNEA KMWYMQALGL LGDKPVSIFS NGWENPSLSN AADKTQAKQF HDEISRIRSG GLLPDVRTAN TLTGLFRPQQ NEK LLGYWQ MLEMRLFNLR NNLSIDGQPL SLPVFAAPAD PAALLSAAAA ASGGSKPLPS ADIPAMRFPQ ALDSARSLTG QLMQ FGSTL LGLIERRDAE AMSELLQNQA GELMLSSLRM QEQALTELDA EKKILEQSRA GAQSRVDSYR ALYDENVSAE EKRTM DLYL SSAILSTSIG VLDMAAAAAD MAPNIFGVAV GGSRWGGIPK AIGAGMSLAA SATKITADNI SQSEAWRRRR QEWEIQ KNN AESEIRQIDA QLEALAVRRT ATEMQREHME IQQAQTQAQL EFLQRKFSNK ALYSWLRGRL ASIYYRFYDL TAARCMM AE KAYAWQTNDT ATRYIKSGAW QSNNAGLMAG ESLLLNLAEM EQAWLKRDSR SLEVTRTVSL AAVYRTDNVT LAEGIADL L KGNGSGNIPA STGLSMTADN QLHAAFNLKA LNIKDDYPEA LGTTRRIKQI SVTLPALVEP YQDMRAIFRY GGNSLPAGC KAIALSHGIN DDGLFRLDFN DGRWLPFEGI PVDDDNSLTL SFPDATGEKQ KPLLLSLTDI IIHIRYTIC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.10 mg/mL |
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Buffer | pH: 8 |
Grid | Model: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3 |
Details | 0.10 mg/ml TcdA4 were pre-applied on the grid for 20s. Subsequently, the grid was manually blotted and 0.30 mg/ml porcine mucosa heparin was applied and incubated for 2 min. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 5549 / Average electron dose: 100.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |