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- EMDB-48372: Xenorhabdus nematophilus XptA2, wild type State 2 -

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Basic information

Entry
Database: EMDB / ID: EMD-48372
TitleXenorhabdus nematophilus XptA2, wild type State 2
Map dataXenorhabdus nematophilus XptA2, wild type State 2
Sample
  • Complex: A subunit of ABC Toxin Complex
    • Protein or peptide: XptA2 protein
KeywordsTcA / Pore Forming Toxin / TOXIN
Function / homology
Function and homology information


: / TcdA1, receptor binding domain / ABC toxin, N-terminal domain / ABC toxin N-terminal region / 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 ...: / TcdA1, receptor binding domain / ABC toxin, N-terminal domain / ABC toxin N-terminal region / 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
Biological speciesXenorhabdus nematophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsAller SG / Martin CL
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI)P01HL128203 United States
CitationJournal: BioTech (Basel) / Year: 2025
Title: Evaluating TcAs for Use in Biotechnology Applications.
Authors: Cole L Martin / John H Hill / Brian D Wright / Solana R Fernandez / Aubrey L Miller / Karina J Yoon / Suzanne E Lapi / Stephen G Aller /
Abstract: ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with (Bt) toxins, and as such, they have been highly ...ABC toxin complexes (Tcs) are tripartite complexes that come together to form nano-syringe-like translocation systems. ABC Tcs are often compared with (Bt) toxins, and as such, they have been highly studied as a potential novel pesticide to combat growing insect resistance. Moreover, it is possible to substitute the cytotoxic hypervariable region with alternative peptides, which promise potential use as a novel peptide delivery system. These toxins possess the unique ability to form active chimeric holotoxins across species and display the capability to translocate a variety of payloads across membrane bilayers. Additionally, mutagenesis on the linker region and the receptor binding domains (RBDs) show that mutations do not inherently cause a loss of functionality for translocation. For these reasons, Tcs have emerged as an ideal candidate for targeted protein engineering. However, elucidation of the specific function of each RBD in relation to target receptor recognition currently limits the use of a rational design approach with any ABC Tc. Additionally, there is a distinct lack of targeting and biodistribution data for many Tcs among mammals and mammalian cell lines. Here, we outline two separate strategies for modifying the targeting capabilities of the A subunit (TcA) from , Xn-XptA2. We identify novel structural differences that make Xn-XptA2 different than other characterized TcAs and display the modular capabilities of substituting RBDs from alternative TcAs into the Xn-XptA2 scaffold. Finally, we show the first, to our knowledge, biodistribution data of any TcA in mice.
History
DepositionDec 19, 2024-
Header (metadata) releaseJan 15, 2025-
Map releaseJan 15, 2025-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48372.png

Downloads & links

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Map

FileDownload / File: emd_48372.map.gz / Format: CCP4 / Size: 158 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXenorhabdus nematophilus XptA2, wild type State 2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.27 Å/pix.
x 346 pix.
= 438.728 Å		1.27 Å/pix.
x 346 pix.
= 438.728 Å		1.27 Å/pix.
x 346 pix.
= 438.728 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.268 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00379
Minimum - Maximum-0.02700393 - 0.045583252
Average (Standard dev.)0.00023470976 (±0.0019985505)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions346346346
Spacing346346346
CellA=B=C: 438.728 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_48372_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_48372_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : A subunit of ABC Toxin Complex

EntireName: A subunit of ABC Toxin Complex
Components
  • Complex: A subunit of ABC Toxin Complex
    • Protein or peptide: XptA2 protein

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Supramolecule #1: A subunit of ABC Toxin Complex

SupramoleculeName: A subunit of ABC Toxin Complex / 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: XptA2 protein

MacromoleculeName: XptA2 protein / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Xenorhabdus nematophila (bacteria)
Molecular weightTheoretical: 284.392188 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MYSTAVLLNK ISPTRDGQTM TLADLQYLSF SELRKIFDDQ LSWGEARHLY HETIEQKKNN RLLEARIFTR ANPQLSGAIR LGIERDSVS RSYDEMFGAR SSSFVKPGSV ASMFSPAGYL TELYREAKDL HFSSSAYHLD NRRPDLADLT LSQSNMDTEI S TLTLSNEL ...String:
MYSTAVLLNK ISPTRDGQTM TLADLQYLSF SELRKIFDDQ LSWGEARHLY HETIEQKKNN RLLEARIFTR ANPQLSGAIR LGIERDSVS RSYDEMFGAR SSSFVKPGSV ASMFSPAGYL TELYREAKDL HFSSSAYHLD NRRPDLADLT LSQSNMDTEI S TLTLSNEL LLEHITRKTG GDSDALMESL STYRQAIDTP YHQPYETIRQ VIMTHDSTLS ALSRNPEVMG QAEGASLLAI LA NISPELY NILTEEITEK NADALFAQNF SENITPENFA SQSWIAKYYG LELSEVQKYL GMLQNGYSDS TSAYVDNIST GLV VNNESK LEAYKITRVK TDDYDKNINY FDLMYEGNNQ FFIRANFKVS REFGATLRKN AGPSGIVGSL SGPLIANTNF KSNY LSNIS DSEYKNGVKI YAYRYTSSTS ATNQGGGIFT FESYPLTIFA LKLNKAIRLC LTSGLSPNEL QTIVRSDNAQ GIIND SVLT KVFYTLFYSH RYALSFDDAQ VLNGSVINQY ADDDSVSHFN RLFNTPPLKG KIFEADGNTV SIDPDEEQST FARSAL MRG LGVNSGELYQ LGKLAGVLDA QNTITLSVFV ISSLYRLTLL ARVHQLTVNE LCMLYGLSPF NGKTTASLSS GELPRLV IW LYQVTQWLTE AEITTEAIWL LCTPEFSGNI SPEISNLLNN LRPSISEDMA QSHNRELQAE ILAPFIAATL HLASPDMA R YILLWTDNLR PGGLDIAGFM TLVLKESLNA NETTQLVQFC HVMAQLSLSV QTLRLSEAEL SVLVISGFAV LGAKNQPAG QHNIDTLFSL YRFHQWINGL GNPGSDTLDM LRQQTLTADR LASVMGLDIS MVTQAMVSAG VNQLQCWQDI NTVLQWIDVA SALHTMPSV IRTLVNIRYV TALNKAESNL PSWDEWQTLA ENMEAGLSTQ QAQTLADYTA ERLSSVLCNW FLANIQPEGV S LHSRDDLY SYFLIDNQVS SAIKTTRLAE AIAGIQLYIN RALNRIEPNA RADVSTRQFF TDWTVNNRYS TWGGVSRLVY YP ENYIDPT QRIGQTRMMD ELLENISQSK LSRDTVEDAF KTYLTRFETV ADLKVVSAYH DNVNSNTGLT WFVGQTRENL PEY YWRNVD ISRMQAGELA ANAWKEWTKI DTAVNPYKDA IRPVIFRERL HLIWVEKEEV AKNGTDPVET YDRFTLKLAF LRHD GSWSA PWSYDITTQV EAVTDKKPDT ERLALAASGF QGEDTLLVFV YKTGKSYSDF GGSNKNVAGM TIYGDGSFKK MENTA LSRY SQLKNTFDII HTQGNDLVRK ASYRFAQDFE VPASLNMGSA IGDDSLTVME NGNIPQITSK YSSDNLAITL HNAAFT VRY DGSGNVIRNK QISAMKLTGV DGKSQYGNAF IIANTVKHYG GYSDLGGPIT VYNKTKNYIA SVQGHLMNAD YTRRLIL TP VENNYYARLF EFPFSPNTIL NTVFTVGSNK TSDFKKCSYA VDGNNSQGFQ IFSSYQSSGW LDIDTGINNT DIKITVMA G SKTHTFTASD HIASLPANSF DAMPYTFKPL EIDASSLAFT NNIAPLDIVF ETKAKDGRVL GKIKQTLSVK RVNYNPEDI LFLRETHSGA QYMQLGVYRI RLNTLLASQL VSRANTGIDT ILTMETQRLP EPPLGEGFFA NFVLPKYDPA EHGDERWFKI HIGNVGGNT GRQPYYSGML SDTSETSMTL FVPYAEGYYM HEGVRLGVGY QKITYDNTWE SAFFYFDETK QQFVLINDAD H DSGMTQQG IVKNIKKYKG FLNVSIATGY SAPMDFNSAS ALYYWELFYY TPMMCFQRLL QEKQFDEATQ WINYVYNPAG YI VNGEIAP WIWNCRPLEE TTSWNANPLD AIDPDAVAQN DPMHYKIATF MRLLDQLILR GDMAYRELTR DALNEAKMWY VRT LELLGD EPEDYGSQQW AAPSLSGAAS QTVQAAYQQD LTMLGRGGVS KNLRTANSLV GLFLPEYNPA LTDYWQTLRL RLFN LRHNL SIDGQPLSLA IYAEPTDPKA LLTSMVQASQ GGSAVLPGTL SLYRFPVMLE RTRNLVAQLT QFGTSLLSMA EHDDA DELT TLLLQQGMEL ATQSIRIQQR TVDEVDADIA VLAESRRSAQ NRLEKYQQLY DEDINHGEQR AMSLLDAAAG QSLAGQ VLS IAEGVADLVP NVFGLACGGS RWGAALRASA SVMSLSATAS QYSADKISRS EAYRRRRQEW EIQRDNADGE VKQMDAQ LE SLKIRREAAQ MQVEYQETQQ AHTQAQLELL QRKFTNKALY SWMRGKLSAI YYQFFDLTQS FCLMAQEALR RELTDNGV T FIRGGAWNGT TAGLMAGETL LLNLAEMEKV WLERDERALE VTRTVSLAQF YQALSSDNFN LTEKLTQFLR EGKGNVGAS GNELKLSNRQ IEASVRLSDL KIFSDYPESL GNTRQLKQVS VTLPALVGPY EDIRAVLNYG GSIVMPRGCS AIALSHGVND SGQFMLDFN DSRYLPFEGI SVNDSGSLTL SFPDATDRQK ALLESLSDII LHIRYTIRS

UniProtKB: XptA2 protein

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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

Concentration2 mg/mL
BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI POLARA 300
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 75.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.5 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 42561
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION
Final 3D classificationSoftware - Name: RELION

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