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- EMDB-10034: Cryo-EM structure of Xenorhabdus nematophila XptA1 -

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Basic information

Entry
Database: EMDB / ID: EMD-10034
TitleCryo-EM structure of Xenorhabdus nematophila XptA1
Map dataCryo-EM density map of Xenorhabdus nematophila XptA1
Sample
  • Complex: XptA1 pentamer
    • Protein or peptide: A component of insecticidal toxin complex (Tc)
KeywordsToxin / membrane permeation / translocation / complex
Function / homology
Function and homology information


TcA 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
Similarity search - Domain/homology
A component of insecticidal toxin complex (Tc) / A component of insecticidal toxin complex (Tc)
Similarity search - Component
Biological speciesXenorhabdus nematophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsRoderer D / Leidreiter F
Funding support Germany, 1 items
OrganizationGrant numberCountry
European Research Council615984 Germany
CitationJournal: Sci Adv / Year: 2019
Title: Common architecture of Tc toxins from human and insect pathogenic bacteria.
Authors: F Leidreiter / D Roderer / D Meusch / C Gatsogiannis / R Benz / S Raunser /
Abstract: Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution ...Tc toxins use a syringe-like mechanism to penetrate the membrane and translocate toxic enzymes into the host cytosol. They are composed of three components: TcA, TcB, and TcC. Low-resolution structures of TcAs from different bacteria suggest a considerable difference in their architecture and possibly in their mechanism of action. Here, we present high-resolution structures of five TcAs from insect and human pathogens, which show a similar overall composition and domain organization. Essential structural features, including a trefoil protein knot, are present in all TcAs, suggesting a common mechanism of action. All TcAs form functional pores and can be combined with TcB-TcC subunits from other species to form active chimeric holotoxins. We identified a conserved ionic pair that stabilizes the shell, likely operating as a strong latch that only springs open after destabilization of other regions. Our results provide new insights into the architecture and mechanism of the Tc toxin family.
History
DepositionJun 4, 2019-
Header (metadata) releaseOct 23, 2019-
Map releaseOct 23, 2019-
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
  • Download
  • 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-6rw8
  • Surface level: 0.028
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_10034.png

Downloads & links

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Map

FileDownload / File: emd_10034.map.gz / Format: CCP4 / Size: 244.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM density map of Xenorhabdus nematophila XptA1
Voxel sizeX=Y=Z: 1.14 Å
Density
Contour LevelBy AUTHOR: 0.028 / Movie #1: 0.028
Minimum - Maximum-0.040336102 - 0.12986967
Average (Standard dev.)0.00049508276 (±0.0049487688)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 456.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z400400400
origin x/y/z0.0000.0000.000
length x/y/z456.000456.000456.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS400400400
D min/max/mean-0.0400.1300.000

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Supplemental data

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Sample components

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Entire : XptA1 pentamer

EntireName: XptA1 pentamer
Components
  • Complex: XptA1 pentamer
    • Protein or peptide: A component of insecticidal toxin complex (Tc)

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Supramolecule #1: XptA1 pentamer

SupramoleculeName: XptA1 pentamer / 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

BufferpH: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average exposure time: 1.5 sec. / Average electron dose: 60.0 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

Startup modelType of model: EMDB MAP
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 218992
Initial angle assignmentType: OTHER / Software - Name: SPHIRE
Final angle assignmentType: OTHER / Software - Name: SPHIRE

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Atomic model buiding 1

Initial modelPDB ID:

1vw1
PDB Unreleased entry


Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-6rw8:
Cryo-EM structure of Xenorhabdus nematophila XptA1

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