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- EMDB-10794: Photorhabdus luminescens TcdA1 in complex with BSA-Lewis X -

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Basic information

Entry
Database: EMDB / ID: EMD-10794
TitlePhotorhabdus luminescens TcdA1 in complex with BSA-Lewis X
Map dataThe main map of Pl-TcdA1 with BSA-LewisX after postprocessing
Sample
  • Complex: Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, crosslinked with glutaraldehyde
    • Complex: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
      • Protein or peptide: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
    • Complex: BSA with Lewis X glycans crosslinked to surface lysines
      • Protein or peptide: BSA with Lewis X glycans crosslinked to surface lysines
Biological speciesPhotorhabdus luminescens (bacteria) / Bos taurus (cattle)
Methodsingle particle reconstruction / cryo EM / Resolution: 5.0 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 releaseSep 2, 2020-
UpdateMar 17, 2021-
Current statusMar 17, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10794.png

Downloads & links

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Map

FileDownload / File: emd_10794.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe main map of Pl-TcdA1 with BSA-LewisX after postprocessing
Voxel sizeX=Y=Z: 1.11 Å
Density
Contour LevelBy AUTHOR: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.020802047 - 0.049993984
Average (Standard dev.)0.0004675394 (±0.0030881853)
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-0.0210.0500.000

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Supplemental data

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Sample components

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Entire : Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, cro...

EntireName: Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, crosslinked with glutaraldehyde
Components
  • Complex: Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, crosslinked with glutaraldehyde
    • Complex: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
      • Protein or peptide: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
    • Complex: BSA with Lewis X glycans crosslinked to surface lysines
      • Protein or peptide: BSA with Lewis X glycans crosslinked to surface lysines

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Supramolecule #1: Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, cro...

SupramoleculeName: Photorhabdus luminescens TcdA1 pentamer with one BSA-Lewis X, crosslinked with glutaraldehyde
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Molecular weightTheoretical: 1.5 MDa

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Supramolecule #2: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer

SupramoleculeName: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: BSA with Lewis X glycans crosslinked to surface lysines

SupramoleculeName: BSA with Lewis X glycans crosslinked to surface lysines
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Bos taurus (cattle)

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Macromolecule #1: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer

MacromoleculeName: Photorhabdus luminescens toxin complex subunit TcdA1, Homopentamer
type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKR ANPQLQNAVH LAILAPNAEL IGYNNQFSGR ASQYVAPGTV SSMFSPAAYL T ELYREARN LHASDSVYYL DTRRPDLKSM ALSQQNMDIE LSTLSLSNEL ...String:
MNESVKEIPD VLKSQCGFNC LTDISHSSFN EFRQQVSEHL SWSETHDLYH DAQQAQKDNR LYEARILKR ANPQLQNAVH LAILAPNAEL IGYNNQFSGR ASQYVAPGTV SSMFSPAAYL T ELYREARN LHASDSVYYL DTRRPDLKSM ALSQQNMDIE LSTLSLSNEL LLESIKTESK LE NYTKVME MLSTFRPSGA TPYHDAYENV REVIQLQDPG LEQLNASPAI AGLMHQASLL GIN ASISPE LFNILTEEIT EGNAEELYKK NFGNIEPASL AMPEYLKRYY NLSDEELSQF IGKA SNFGQ QEYSNNQLIT PVVNSSDGTV KVYRITREYT TNAYQMDVEL FPFGGENYRL DYKFK NFYN ASYLSIKLND KRELVRTEGA PQVNIEYSAN ITLNTADISQ PFEIGLTRVL PSGSWA YAA AKFTVEEYNQ YSFLLKLNKA IRLSRATELS PTILEGIVRS VNLQLDINTD VLGKVFL TK YYMQRYAIHA ETALILCNAP ISQRSYDNQP SQFDRLFNTP LLNGQYFSTG DEEIDLNS G STGDWRKTIL KRAFNIDDVS LFRLLKITDH DNKDGKIKNN LKNLSNLYIG KLLADIHQL TIDELDLLLI AVGEGKTNLS AISDKQLATL IRKLNTITSW LHTQKWSVFQ LFIMTSTSYN KTLTPEIKN LLDTVYHGLQ GFDKDKADLL HVMAPYIAAT LQLSSENVAH SVLLWADKLQ P GDGAMTAE KFWDWLNTKY TPGSSEAVET QEHIVQYCQA LAQLEMVYHS TGINENAFRL FV TKPEMFG AATGAAPAHD ALSLIMLTRF ADWVNALGEK ASSVLAAFEA NSLTAEQLAD AMN LDANLL LQASIQAQNH QHLPPVTPEN AFSCWTSINT ILQWVNVAQQ LNVAPQGVSA LVGL DYIQS MKETPTYAQW ENAAGVLTAG LNSQQANTLH AFLDESRSAA LSTYYIRQVA KAAAA IKSR DDLYQYLLID NQVSAAIKTT RIAEAIASIQ LYVNRALENV EENANSGVIS RQFFID WDK YNKRYSTWAG VSQLVYYPEN YIDPTMRIGQ TKMMDALLQS VSQSQLNADT VEDAFMS YL TSFEQVANLK VISAYHDNIN NDQGLTYFIG LSETDAGEYY WRSVDHSKFN DGKFAANA W SEWHKIDCPI NPYKSTIRPV IYKSRLYLLW LEQKEITKQT GNSKDGYQTE TDYRYELKL AHIRYDGTWN TPITFDVNKK ISELKLEKNR APGLYCAGYQ GEDTLLVMFY NQQDTLDSYK NASMQGLYI FADMASKDMT PEQSNVYRDN SYQQFDTNNV RRVNNRYAED YEIPSSVSSR K DYGWGDYY LSMVYNGDIP TINYKAASSD LKIYISPKLR IIHNGYEGQK RNQCNLMNKY GK LGDKFIV YTSLGVNPNN SSNKLMFYPV YQYSGNTSGL NQGRLLFHRD TTYPSKVEAW IPG AKRSLT NQNAAIGDDY ATDSLNKPDD LKQYIFMTDS KGTATDVSGP VEINTAISPA KVQI IVKAG GKEQTFTADK DVSIQPSPSF DEMNYQFNAL EIDGSGLNFI NNSASIDVTF TAFAE DGRK LGYESFSIPV TLKVSTDNAL TLHHNENGAQ YMQWQSYRTR LNTLFARQLV ARATTG IDT ILSMETQNIQ EPQLGKGFYA TFVIPPYNLS THGDERWFKL YIKHVVDNNS HIIYSGQ LT DTNINITLFI PLDDVPLNQD YHAKVYMTFK KSPSDGTWWG PHFVRDDKGI VTINPKSI L THFESVNVLN NISSEPMDFS GANSLYFWEL FYYTPMLVAQ RLLHEQNFDE ANRWLKYVW SPSGYIVHGQ IQNYQWNVRP LLEDTSWNSD PLDSVDPDAV AQHDPMHYKV STFMRTLDLL IARGDHAYR QLERDTLNEA KMWYMQALHL LGDKPYLPLS TTWSDPRLDR AADITTQNAH D SAIVALRQ NIPTPAPLSL RSANTLTDLF LPQINEVMMN YWQTLAQRVY NLRHNLSIDG QP LYLPIYA TPADPKALLS AAVATSQGGG KLPESFMSLW RFPHMLENAR GMVSQLTQFG STL QNIIER QDAEALNALL QNQAAELILT NLSIQDKTIE ELDAEKTVLE KSKAGAQSRF DSYG KLYDE NINAGENQAM TLRASAAGLT TAVQASRLAG AAADLVPNIF GFAGGGSRWG AIAEA TGYV MEFSANVMNT EADKISQSET YRRRRQEWEI QRNNAEAELK QIDAQLKSLA VRREAA VLQ KTSLKTQQEQ TQSQLAFLQR KFSNQALYNW LRGRLAAIYF QFYDLAVARC LMAEQAY RW ELNDDSARFI KPGAWQGTYA GLLAGETLML SLAQMEDAHL KRDKRALEVE RTVSLAEV Y AGLPKDNGPF SLAQEIDKLV SQGSGSAGSG NNNLAFGAGT DTKTSLQASV SFADLKIRE DYPASLGKIR RIKQISVTLP ALLGPYQDVQ AILSYGDKAG LANGCEALAV SHGMNDSGQF QLDFNDGKF LPFEGIAIDQ GTLTLSFPNA SMPEKGKQAT MLKTLNDIIL HIRYTIK

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Macromolecule #2: BSA with Lewis X glycans crosslinked to surface lysines

MacromoleculeName: BSA with Lewis X glycans crosslinked to surface lysines
type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Bos taurus (cattle)
SequenceString: MKWVTFISLL LLFSSAYSRG VFRRDTHKSE IAHRFKDLGE EHFKGLVLIA FSQYLQQCPF DEHVKLVNE LTEFAKTCVA DESHAGCEKS LHTLFGDELC KVASLRETYG DMADCCEKQE P ERNECFLS HKDDSPDLPK LKPDPNTLCD EFKADEKKFW GKYLYEIARR ...String:
MKWVTFISLL LLFSSAYSRG VFRRDTHKSE IAHRFKDLGE EHFKGLVLIA FSQYLQQCPF DEHVKLVNE LTEFAKTCVA DESHAGCEKS LHTLFGDELC KVASLRETYG DMADCCEKQE P ERNECFLS HKDDSPDLPK LKPDPNTLCD EFKADEKKFW GKYLYEIARR HPYFYAPELL YY ANKYNGV FQECCQAEDK GACLLPKIET MREKVLASSA RQRLRCASIQ KFGERALKAW SVA RLSQKF PKAEFVEVTK LVTDLTKVHK ECCHGDLLEC ADDRADLAKY ICDNQDTISS KLKE CCDKP LLEKSHCIAE VEKDAIPENL PPLTADFAED KDVCKNYQEA KDAFLGSFLY EYSRR HPEY AVSVLLRLAK EYEATLEECC AKDDPHACYS TVFDKLKHLV DEPQNLIKQN CDQFEK LGE YGFQNALIVR YTRKVPQVST PTLVEVSRSL GKVGTRCCTK PESERMPCTE DYLSLIL NR LCVLHEKTPV SEKVTKCCTE SLVNRRPCFS ALTPDETYVP KAFDEKLFTF HADICTLP D TEKQIKKQTA LVELLKHKPK ATEEQLKTVM ENFVAFVDKC CAADDKEACF AVEGPKLVV STQTALA

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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

Concentration0.06 mg/mL
BufferpH: 8
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 293 K / Instrument: GATAN CRYOPLUNGE 3
DetailsThe sample was crosslinked with glutaraldehyde and subsequently purified by SEC

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 4992 / Average electron dose: 100.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 711872
CTF correctionSoftware - Name: SPHIRE
Initial angle assignmentType: NOT APPLICABLE / Software - Name: SPHIRE
Final 3D classificationSoftware - Name: SPHIRE
Final angle assignmentType: NOT APPLICABLE / Software - Name: SPHIRE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 5.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 199038

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: RIGID BODY FIT

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