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- EMDB-20053: Cryo-EM structure of YenTcA in its prepore state -

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Basic information

Entry
Database: EMDB / ID: EMD-20053
TitleCryo-EM structure of YenTcA in its prepore state
Map dataem-volume_P1
Sample
  • Complex: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
    • Protein or peptide: Toxin subunit YenA1
    • Protein or peptide: Toxin subunit YenA2
    • Protein or peptide: Chitinase 2
KeywordsMembrane protein Pore-forming toxin Complex / TOXIN
Function / homology
Function and homology information


chitinase / chitinase activity / chitin catabolic process / chitin binding / : / polysaccharide catabolic process / extracellular region
Similarity search - Function
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 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. ...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 / Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Toxin subunit YenA1 / Toxin subunit YenA2 / Chitinase 2
Similarity search - Component
Biological speciesYersinia entomophaga (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPiper SJ / Brillault L
Funding support Australia, New Zealand, 4 items
OrganizationGrant numberCountry
Australian Research Council (ARC)DP170104484 Australia
Australian Research Council (ARC)DP160101018 Australia
Royal Society of New Zealand14-UOA-146 New Zealand
Foundation for Science and TechnologyC10X0804 New Zealand
CitationJournal: Nat Commun / Year: 2019
Title: Cryo-EM structures of the pore-forming A subunit from the Yersinia entomophaga ABC toxin.
Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren ...Authors: Sarah J Piper / Lou Brillault / Rosalba Rothnagel / Tristan I Croll / Joseph K Box / Irene Chassagnon / Sebastian Scherer / Kenneth N Goldie / Sandra A Jones / Femke Schepers / Lauren Hartley-Tassell / Thomas Ve / Jason N Busby / Julie E Dalziel / J Shaun Lott / Ben Hankamer / Henning Stahlberg / Mark R H Hurst / Michael J Landsberg /
Abstract: ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen ...ABC toxins are pore-forming virulence factors produced by pathogenic bacteria. YenTcA is the pore-forming and membrane binding A subunit of the ABC toxin YenTc, produced by the insect pathogen Yersinia entomophaga. Here we present cryo-EM structures of YenTcA, purified from the native source. The soluble pre-pore structure, determined at an average resolution of 4.4 Å, reveals a pentameric assembly that in contrast to other characterised ABC toxins is formed by two TcA-like proteins (YenA1 and YenA2) and decorated by two endochitinases (Chi1 and Chi2). We also identify conformational changes that accompany membrane pore formation by visualising YenTcA inserted into liposomes. A clear outward rotation of the Chi1 subunits allows for access of the protruding translocation pore to the membrane. Our results highlight structural and functional diversity within the ABC toxin subfamily, explaining how different ABC toxins are capable of recognising diverse hosts.
History
DepositionApr 2, 2019-
Header (metadata) releaseMay 8, 2019-
Map releaseMay 8, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 7.5
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 7.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6ogd
  • Surface level: 7.5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_20053.png

Downloads & links

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Map

FileDownload / File: emd_20053.map.gz / Format: CCP4 / Size: 274.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationem-volume_P1
Voxel sizeX=Y=Z: 1.34 Å
Density
Contour LevelBy AUTHOR: 7.5 / Movie #1: 7.5
Minimum - Maximum-45.992274999999999 - 58.495677999999998
Average (Standard dev.)0.0041607455 (±1.6544155)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions416416416
Spacing416416416
CellA=B=C: 557.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.341.341.34
M x/y/z416416416
origin x/y/z0.0000.0000.000
length x/y/z557.440557.440557.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS416416416
D min/max/mean-45.99258.4960.004

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Supplemental data

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Sample components

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Entire : Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-...

EntireName: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
Components
  • Complex: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
    • Protein or peptide: Toxin subunit YenA1
    • Protein or peptide: Toxin subunit YenA2
    • Protein or peptide: Chitinase 2

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Supramolecule #1: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-...

SupramoleculeName: Yersinia entomophaga toxin complex subunit A (YenTcA) in the pre-pore form
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Yersinia entomophaga (bacteria) / Strain: MH96
Molecular weightTheoretical: 2.08 MDa

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Macromolecule #1: Toxin subunit YenA1

MacromoleculeName: Toxin subunit YenA1 / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 129.91232 KDa
SequenceString: MDKYNNYSNV IKNKSSISPL LAAAAKIEPE ITVLSSASKS NRSQYSQSLA DTLLGLGYRS IFDIAKVSRQ RFIKRHDESL LGNGAVIFD KAVSMANQVL QKYRKNRLEK SNSPLVPQTS SSTDASSESQ TNKLPEYNQL FPEPWDNFCR PGAIEALDSP A SYLLDLYK ...String:
MDKYNNYSNV IKNKSSISPL LAAAAKIEPE ITVLSSASKS NRSQYSQSLA DTLLGLGYRS IFDIAKVSRQ RFIKRHDESL LGNGAVIFD KAVSMANQVL QKYRKNRLEK SNSPLVPQTS SSTDASSESQ TNKLPEYNQL FPEPWDNFCR PGAIEALDSP A SYLLDLYK FIQSVELDGS NQARKLETRR ADIPKLSLDN DALYKEVTAL SIVNDVLSGS AREYIDQSGQ ADKAVNQILG DT HFPFTLP YSLPTQQINK GLGASNIELG TVIQRVDPQF SWNTTQEKYN QVLLAYTQLS SEQIALLSLP DVFTQNFLTQ TEL SAGYLS ASTTEILAEK DLSRHGYIVK AADNIKGPTQ LVEHSDASYD VIELTCTNQA KETITVKLRG ENIITYQRTK ARMV PFDNS SPFSRQLKLT FVAEDNPSLG NLDKGPYFAN MDIYAAEWVR ENVSSETMVS RPFLTMTYRI AIAKAGASLE ELQPE ADAF FINNFGLSAE DSSQLVKLVA FGDQTGSKAE EIESLLSCGE NLPIVSPNVI FANPIFGSYF NDEPFPAPYH FGGVYI NAH QRNAMTIIRA EGGREIQSLS NFRLERLNRF IRLQRWLDLP SHQLDLLLTS VMQADADNSQ QEITEPVLKS LGLFRHL NL QYKITPEIFS SWLYQLTPFA VSGEIAFFDR IFNREQLFDQ PFILDGGSFT YLDAKGSDAK SVKQLCAGLN ISAVTFQF I APLVQSALGL EAGTLVRSFE VVSSLYRLVS IPQTFGLSTE DGLILMNILT DEMGYLAKQP AFDDKQTQDK DFLSIILKM EALSAWLTKN NLTPASLALL LGVTRLAVVP TNNMVTFFKG IANGLSENVC LTTDDFQRQE LEGADWWTLL STNQVIDDMG LVLDIHPVW GKSDEEMLME KIQSIGVSND NNTLSIIVQI LIQAKNAQEN LLSQTISAEY GVERSVVPLQ LRWLGSNVYS V LNQVLNNT PTDISSIVPK LSELTYSLLI YTQLINSLKL NKEFIFLRLT QPNWLGLTQP KLSTQLSLPE IYLITCYQDW VV NANKNED SIHEYLEFAN IKKTEAEKTL VDNSEKCAEL LAEILAWDAG EILKAASLLG LNPPQATNVF EIDWIRRLQT LSE KTMIST EYLWQMGDLT ENSEFSLKEG VGEAVMAALK AQGDSDNV

UniProtKB: Toxin subunit YenA1

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Macromolecule #2: Toxin subunit YenA2

MacromoleculeName: Toxin subunit YenA2 / type: protein_or_peptide / ID: 2 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 156.324938 KDa
SequenceString: MSNSIEAKLQ EDLRDALVDY YLGQIVPNSK DFTNLRSTIK NVDDLYDHLL LDTQVSAKVI TSRLSLVTQS VQQYINRIAL NLEPGLSIN QQEATDWEEF ANRYGYWAAN QQLRMFPEIY VDPTLRLTKT EFFFQLESAL NQGKLTDDVA QKAVLGYLNN F EEVSNLEI ...String:
MSNSIEAKLQ EDLRDALVDY YLGQIVPNSK DFTNLRSTIK NVDDLYDHLL LDTQVSAKVI TSRLSLVTQS VQQYINRIAL NLEPGLSIN QQEATDWEEF ANRYGYWAAN QQLRMFPEIY VDPTLRLTKT EFFFQLESAL NQGKLTDDVA QKAVLGYLNN F EEVSNLEI IAGYQDGIDI ENDKTYFVAR TRMQPYRYFW RSLDASQRNA NSQELYPTAW SEWKAISVPL ENVANGIVRP IM MDNRLYI SWFEVAEEKE TDSDGNIIVS GRYRTKIRLA HLGFDGVWSS GTTLREEVLA DQMEEMIAVV DRMEDEPRLA LVA FKEMSE SWDVVFSYIC DSMLIESSNL PTTTHPPKPG DGDKGLSDLD DYGANLVWFY LHETANGGKA EYKQLILYPV IINR DWPIE LDKTHQGDFG TVDDFTLNSN YTGDELSLYL QSSSTYKYDF SKSKNIIYGI WKEDANNNRC WLNYKLLTPE DYEPQ INAT LVMCDKGDVN IITGFSLPNG GVDAGGKIKV TLRVGKKLRD KFQIKQFSQT QYLQFPEASS ADVWYIGKQI RLNTLF AKE LIGKASRSLD LVLSWETQNS RLEEAILGGA AELIDLDGAN GIYFWELFFH MPFMVSWRFN VEQRYEDANR WVKYLFN PF ECEDEPALLL GKPPYWNSRP LVDEPFKGYS LTQPSDPDAI AASDPIHYRK AVFNFLTKNI IDQGDMEYRK LQPSARTL A RLSYSTASSL LGRRPDVQLT SFWQPLTLED ASYKTDSEIR AIEMQSQPLT FEPVVHDQTM SAVDNDIFMY PMNNELRGL WDRIENRIYN LRHNLTLDGK EINMDLYDSS ISPRGLMKQR YQRVVTARNA SKMNFKVPNY RFEPMLNRSK SGVETLIQFG STLLSLLER KDSLSFDAYQ MIQSGDLYRF SIDLQQQDID INKASLEALQ VSKQSAQDRY DHFKELYDEN ISSTEQKVIE L QSQAANSL LMAQGMRTAA AALDVIPNIY GLAVGGSHWG APLNAAAEII MIKYQADSSK SESLSVSESY RRRRQEWELQ YK QAEWEVN SVEQQINLQN MQIKAANKRL EQVEAQQQQA MALLDYFSER FTNESLYTWL ISQLSSLYLQ AYDAVLSLCL SAE ASLLYE LNLGEQSFVG GGGWNDLYQG LMAGETLKLA LMRMERVYVE QNSRRQEITK TISLKALLGE SWPAELNKLK QKTP INFNL EEQIFVEDYQ ELYQRRIKSV SVSLPMLVGP YEDVCAQLTQ TSSSYSTRAD LKTVENMLTK RTFADTPHLV RSIQP NQQI SLSTGVNDSG LFMLNFDDER FLPFEGSGVD SSWRLQFTNL KQNLDSLNDV ILHVKYTAAI GSSTFSQGVR KILANI NND E

UniProtKB: Toxin subunit YenA2

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Macromolecule #3: Chitinase 2

MacromoleculeName: Chitinase 2 / type: protein_or_peptide / ID: 3 / Number of copies: 5 / Enantiomer: LEVO / EC number: chitinase
Source (natural)Organism: Yersinia entomophaga (bacteria)
Molecular weightTheoretical: 69.740609 KDa
SequenceString: MVNKYTYTSS KAMSDISDVI GEPLAAWDSQ VGGRVFNVIF DGKVYTNTYW VERWQVPGIG SSDGNPHNAW KFVRAATADE INKIGNPTT ADVKPTENIP SPILVEDKYT EETYSRPDVN FKEDGSQGNL SYTATRVCAP MYNHYVGDKT KPKLSAYITD W CQYDARLD ...String:
MVNKYTYTSS KAMSDISDVI GEPLAAWDSQ VGGRVFNVIF DGKVYTNTYW VERWQVPGIG SSDGNPHNAW KFVRAATADE INKIGNPTT ADVKPTENIP SPILVEDKYT EETYSRPDVN FKEDGSQGNL SYTATRVCAP MYNHYVGDKT KPKLSAYITD W CQYDARLD GGGSKEEERG RGFDLATLMQ NPATYDRLIF SFLGICGDIG NKSKKVQEVW DGWNAQAPSL GLPQIGKGHI VP LDPYGDL GTARNVGLPP ESADTSIESG TFLPYYQQNR AAGLLGGLRE LQKKAHAMGH KLDLAFSIGG WSLSSYFSAL AEN PDERRV FVASVVDFFV RFPMFSCVDI DWEYPGGGGD EGNISSDKDG ENYVLLIKEL RSALDSRFGY SNRKEISIAC SGVK AKLKK SNIDQLVANG LDNIYLMSYD FFGTIWADYI GHHTNLYSPK DPGEQELFDL SAEAAIDYLH NELGIPMEKI HLGYA NYGR SAVGGDLTTR QYTKNGPALG TMENGAPEFF DIVKNYMDAE HSLSMGKNGF VLMTDTNADA DFLFSEAKGH FISLDT PRT VKQKGEYAAK NKLGGVFSWS GDQDCGLLAN AAREGLGYVA DSNQETIDMG PLYNPGKEIY LKSISEIKSK

UniProtKB: Chitinase 2

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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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 80.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 19713
Startup modelType of model: EMDB MAP
EMDB ID:

1978

Initial angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.2)
Final angle assignmentType: PROJECTION MATCHING / Software - Name: EMAN (ver. 2.2)
Final reconstructionApplied symmetry - Point group: C5 (5 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: EMAN (ver. 2.2) / Number images used: 9856
FSC plot (resolution estimation)

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