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- EMDB-10797: Xenorhabdus nematophila XptA1 in complex with porcine mucosa heparin -

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Basic information

Entry
Database: EMDB / ID: EMD-10797
TitleXenorhabdus nematophila XptA1 in complex with porcine mucosa heparin
Map data
Sample
  • Complex: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mucosa heparin
    • Protein or peptide: A component of insecticidal toxin complex (Tc)
Keywordstoxin / complex / glycan
Function / homologyTcA receptor binding domain / TcA receptor binding domain / Insecticidal toxin complex/plasmid virulence protein / Tc toxin complex TcA, C-terminal TcB-binding domain / Neuraminidase-like domain / Salmonella virulence plasmid 28.1kDa A protein / Tc toxin complex TcA C-terminal TcB-binding domain / Neuraminidase-like domain / A component of insecticidal toxin complex (Tc)
Function and homology information
Biological speciesXenorhabdus nematophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.7 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: 0.028
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.028
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6yey
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10797.png

Downloads & links

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Map

FileDownload / File: emd_10797.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.21 Å/pix.
x 400 pix.
= 484. Å		1.21 Å/pix.
x 400 pix.
= 484. Å		1.21 Å/pix.
x 400 pix.
= 484. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.06034702 - 0.110892
Average (Standard dev.)0.00044000463 (±0.0045329314)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 484.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.211.211.21
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z484.000484.000484.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0600.1110.000

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Supplemental data

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Sample components

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Entire : Xenorhabdus nematophila XptA1 pentamer in complex with porcine mu...

EntireName: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mucosa heparin
Components
  • Complex: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mucosa heparin
    • Protein or peptide: A component of insecticidal toxin complex (Tc)

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Supramolecule #1: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mu...

SupramoleculeName: Xenorhabdus nematophila XptA1 pentamer in complex with porcine mucosa heparin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenorhabdus nematophila (bacteria)
Molecular weightTheoretical: 1.4 MDa

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Macromolecule #1: A component of insecticidal toxin complex (Tc)

MacromoleculeName: A component of insecticidal toxin complex (Tc) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenorhabdus nematophila (bacteria)
Molecular weightTheoretical: 287.120781 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MIKVNELLDK INRKRSGDTL LLTNISFMSF SEFRHRTSGT LTWRETDFLY QQAHQESKQN KLEELRILSR ANPQLANITN LNITPSTLN NSYNSWFYGR AHRFVKPGSI ASIFSPAAYL TELYREAKDF HPDNSQYHLN KRRPDIASLA LTQNNMDEEI S TLSLSNEL ...String:
MIKVNELLDK INRKRSGDTL LLTNISFMSF SEFRHRTSGT LTWRETDFLY QQAHQESKQN KLEELRILSR ANPQLANITN LNITPSTLN NSYNSWFYGR AHRFVKPGSI ASIFSPAAYL TELYREAKDF HPDNSQYHLN KRRPDIASLA LTQNNMDEEI S TLSLSNEL LLHNIQTLEK TDYNGVMKML STYRQTGMTP YHLPYESARQ AILLQDKNLT AFSRNTDVAE LMDPTSLLAI KT DISPELY QILVEEITPE NSTELMKKNF GTDDVLIFKS YASLARYYDL SYDELSLFVN LSFGKKNTNQ QYKNEQLITL VND GNDTAT ARLIKRTRKD FYDSHLNYAE LIPIKENEYK YNFSVKKTEP DHLDFRLQNG DKEYIYQDKN FVPIANTHYS IPIK LTTEQ ITNGITLRLW RVKPNPSDAI NANAHFKMME FPGDIFLLKL NKAIRLYKAT GISPEDIWQV IESIYDDLTI DSNVL GKLF YVQYYMQHYN ISVSDALVLC HSDISQYSTK QQPSHFTMLF NTPLLNGQEF SADNTKLDLT PGESKNHFYL GIMKRA FRV NDTELYTLWK LANGGTNPEF MCSIENLSLL YRVRLLADIH HLTVNELSML LSVSPYVNTK IALFSDTALT QLISFLF QC TQWLTTQKWS VSDVFLMTTD NYSTVLTPDI ENLITTLSNG LSTLSLGDDE LIRAAAPLIA ASIQMDSAKT AETILLWI N QIKPQGLTFD DFMIIAANRD RSENETSNMV AFCQVLGQLS LIVRNIGLSE NELTLLVTKP EKFQSETTAL QHDLPTLQA LTRFHAVIMR CGSYATEILT ALELGALTAE QLAVALKFDA QVVTQALQQT DLGVNTFTNW RTIDVTLQWL DVAATLGITP DGVAALIKL KYVGEPETPM PTFDDWQAAS TLLQAGLNSQ QSDQLQAWLD EATTTAASAY YIKNGAPQQI KSRDELYSYL L IDNQVSAQ VKTTRVAEAI ASIQLYVNRA LNNVEGKVSK PVKTRQFFCD WETYNRRYST WAGVSELAYY PENYIDPTIR IG QTGMMNN LLQQLSQSQL NIDTVEDSFK NYLTAFEDVA NLQVISGYHD SINVNEGLTY LIGYSQTEPR IYYWRNVDHQ KCQ HGQFAA NAWGEWKKIE IPINVWQENI RPVIYKSRLY LLWLEQKELK NESEDGKIDI TDYILKLSHI RYDGSWSSPF NFNV TDKIE NLINKKASIG MYCSSDYEKD VIIVYFHEKK DNYSFNSLPA REGMTINPDM TLSILTENDL DAIVKSTLSE LDTRT EYKV NNQFATDYLA EYKESITTKN KLASFTGNIF DLSYISPGNG HINLTFNPSM EINFSKGNIY NDEVKYLLSM VEDETV ILF DYDRHDEMLG KEEEVFHYGT LDFIISIDLK NAEYFRVLMH LRTKEKIPRK SEIGVGINYD YESNDAEFKL DTNIVLD WK DNTGVWHTIC ESFTNDVSII NNMGNIAALF LREDPCVYLC SIATDIKIAS SMIEQIQDKN ISFLLKNGSD ILVELNAE D HVASKPSHES DPMVYDFNQV KVDIEGYDIP LVSEFIIKQP DGGYNDIVIE SPIHIKLKSK DTSNVISLHK MPSGTQYMQ IGPYRTRLNT LFSRKLAERA NIGIDNVLSM ETQNLPEPQL GEGFYATFKL PPYNKEEHGD ERWFKIHIGN IDGNSARQPY YEGMLSDIE TTVTLFVPYA KGYYIREGVR LGVGYKKIIY DKSWESAFFY FDETKNQFIF INDADHDSGM TQQGIVKNIK K YKGFIHVV VMKNNTEPMD FNGANAIYFW ELFYYTPMMV FQRLLQEQNF TESTRWLRYI WNPAGYSVQG EMQDYYWNVR PL EEDTSWN ANPLDSVDPD AVAQHDPMHY KVATFMKMLD LLITRGDSAY RQLERDTLNE AKMWYVQALT LLGDEPYFSL DND WSEPRL EEAASQTMRH HYQHKMLQLR QRAALPTKRT ANSLTALFLP QINKKLQGYW QTLTQRLYNL RHNLTIDGQP LSLS LYATP ADPSMLLSAA ITASQGGGDL PHAVMPMYRF PVILENAKWG VSQLIQFGNT LLSITERQDA EALAEILQTQ GSELA LQSI KMQDKVMAEI DADKLALQES RHGAQSRFDS FNTLYDEDVN AGEKQAMDLY LSSSVLSTSG TALHMAAAAA DLVPNI YGF AVGGSRFGAL FNASAIGIEI SASATRIAAD KISQSEIYRR RRQEWEIQRN NAEAEIKQID AQLATLAVRR EAAVLQK NY LETQQAQTQA QLAFLQSKFS NAALYNWLRG RLSAIYYQFY DLAVSLCLMA EQTYQYELNN AAAHFIKPGA WHGTYAGL L AGETLMLNLA QMEKSYLEKD ERALEVTRTV SLAEVYAGLT ENSFILKDKV TELVNAGEGS AGTTLNGLNV EGTQLQASL KLSDLNIATD YPDGLGNTRR IKQISVTLPA LLGPYQDVRA ILSYGGSTMM PRGCKAIAIS HGMNDSGQFQ MDFNDAKYLP FEGLPVADT GTLTLSFPGI SGKQKSLLLS LSDIILHIRY TIRS

UniProtKB: A component of insecticidal toxin complex (Tc)

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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: 7.5
GridModel: Quantifoil R2/1 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 285 K / Instrument: FEI VITROBOT MARK IV
Details0.10 mg/ml XptA1 were pre-applied on the grid for 30s. Subsequently, the grid was manually blotted and 0.30 mg/ml porcine mucosa heparin was applied and incubated for 4 min.

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
Image recordingFilm or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Number real images: 1855 / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 346048
Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 172596
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:

6rw8


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 65.8
Output model

PDB-6yey:
Xenorhabdus nematophila XptA1 in complex with porcine mucosa heparin

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