[English] 日本語
Yorodumi
- EMDB-48373: Xenorhabdus nematophilus XptA2 RBD C Chimera -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-48373
TitleXenorhabdus nematophilus XptA2 RBD C Chimera
Map dataXenorhabdus nematophilus XptA2 RBD C Chimera
Sample
  • Complex: XptA2 RBD C Chimera
    • Protein or peptide: A component of insecticidal toxin complex (Tc)
KeywordsTcA / Pore Forming Toxin / TOXIN
Biological speciesXenorhabdus nematophila (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 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) releaseMar 5, 2025-
Map releaseMar 5, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

Downloads & links

-
Map

FileDownload / File: emd_48373.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationXenorhabdus nematophilus XptA2 RBD C Chimera
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.35 Å/pix.
x 360 pix.
= 485.46 Å
1.35 Å/pix.
x 360 pix.
= 485.46 Å
1.35 Å/pix.
x 360 pix.
= 485.46 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3485 Å
Density
Contour LevelBy AUTHOR: 0.0894
Minimum - Maximum-0.40406588 - 0.96236914
Average (Standard dev.)0.00030195492 (±0.03186316)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 485.46 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: Half Map B

Fileemd_48373_half_map_1.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Half map: Half Map A

Fileemd_48373_half_map_2.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

-
Sample components

-
Entire : XptA2 RBD C Chimera

EntireName: XptA2 RBD C Chimera
Components
  • Complex: XptA2 RBD C Chimera
    • Protein or peptide: A component of insecticidal toxin complex (Tc)

-
Supramolecule #1: XptA2 RBD C Chimera

SupramoleculeName: XptA2 RBD C Chimera / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Xenorhabdus nematophila (bacteria)

-
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: 285.458281 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 EPPLGEGFYA TFVIPPYNLS THGDERWFKL YIKHVVDNN SHIIYSGQLT DTNINITLFI PLDDVPLNQD YHAKVYMTFK KSPSDGTWWG PHFVRDDKGI VTINPKSILT H FESVNVLN NYSAPMDFNS ASALYYWELF YYTPMMCFQR LLQEKQFDEA TQWINYVYNP AGYIVNGEIA PWIWNCRPLE ET TSWNANP LDAIDPDAVA QNDPMHYKIA TFMRLLDQLI LRGDMAYREL TRDALNEAKM WYVRTLELLG DEPEDYGSQQ WAA PSLSGA ASQTVQAAYQ QDLTMLGRGG VSKNLRTANS LVGLFLPEYN PALTDYWQTL RLRLFNLRHN LSIDGQPLSL AIYA EPTDP KALLTSMVQA SQGGSAVLPG TLSLYRFPVM LERTRNLVAQ LTQFGTSLLS MAEHDDADEL TTLLLQQGME LATQS IRIQ QRTVDEVDAD IAVLAESRRS AQNRLEKYQQ LYDEDINHGE QRAMSLLDAA AGQSLAGQVL SIAEGVADLV PNVFGL ACG GSRWGAALRA SASVMSLSAT ASQYSADKIS RSEAYRRRRQ EWEIQRDNAD GEVKQMDAQL ESLKIRREAA QMQVEYQ ET QQAHTQAQLE LLQRKFTNKA LYSWMRGKLS AIYYQFFDLT QSFCLMAQEA LRRELTDNGV TFIRGGAWNG TTAGLMAG E TLLLNLAEME KVWLERDERA LEVTRTVSLA QFYQALSSDN FNLTEKLTQF LREGKGNVGA SGNELKLSNR QIEASVRLS DLKIFSDYPE SLGNTRQLKQ VSVTLPALVG PYEDIRAVLN YGGSIVMPRG CSAIALSHGV NDSGQFMLDF NDSRYLPFEG ISVNDSGSL TLSFPDATDR QKALLESLSD IILHIRYTIR SENLYFQGDY KDDDDKLEHH HHHH

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 35.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 77025
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242):Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more