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- EMDB-10796: Morganella morganii TcdA4 in complex with porcine mucosa heparin -

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Basic information

Entry
Database: EMDB / ID: EMD-10796
TitleMorganella morganii TcdA4 in complex with porcine mucosa heparin
Map data
Sample
  • Complex: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin
    • Protein or peptide: Insecticidal toxin protein
Keywordstoxin / complex / glycan
Biological speciesMorganella morganii (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.2 Å
AuthorsRoderer D / Broecker F / Sitsel O / Kaplonek P / Leidreiter F / Seeberger PH / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council (ERC)615984 Germany
CitationJournal: 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
DepositionMar 25, 2020-
Header (metadata) releaseApr 8, 2020-
Map releaseJul 8, 2020-
UpdateMay 22, 2024-
Current statusMay 22, 2024Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.023
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yew
  • Surface level: 0.023
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10796.png

Downloads & links

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Map

FileDownload / File: emd_10796.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.023 / Movie #1: 0.023
Minimum - Maximum-0.066096395 - 0.1614914
Average (Standard dev.)0.0004725108 (±0.0048935087)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 426.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.111.111.11
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z426.240426.240426.240
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0660.1610.000

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Supplemental data

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Sample components

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Entire : Morganella morganii TcdA4 pentamer in complex with porcine mucosa...

EntireName: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin
Components
  • Complex: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin
    • Protein or peptide: Insecticidal toxin protein

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Supramolecule #1: Morganella morganii TcdA4 pentamer in complex with porcine mucosa...

SupramoleculeName: Morganella morganii TcdA4 pentamer in complex with porcine mucosa heparin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Morganella morganii (bacteria)
Molecular weightTheoretical: 1.4 MDa

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Macromolecule #1: Insecticidal toxin protein

MacromoleculeName: Insecticidal toxin protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Morganella morganii (bacteria)
Molecular weightTheoretical: 275.658312 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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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

Concentration0.10 mg/mL
BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3
Details0.10 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.

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 5549 / Average electron dose: 100.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 477602
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 182506
Initial angle assignmentType: NOT APPLICABLE / Software - Name: SPHIRE
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPHIRE

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Atomic model buiding 1

Initial modelPDB ID:

6rw9


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 127.6
Output model

PDB-6yew:
Morganella morganii TcdA4 in complex with porcine mucosa heparin

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