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- EMDB-17440: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin -

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Basic information

Entry
Database: EMDB / ID: EMD-17440
TitlePhotorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
Map dataComposite map used for model building
Sample
  • Complex: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
    • Protein or peptide: Toxin protein
KeywordsBacterial toxin / TOXIN
Function / homologyTcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / Toxin protein
Function and homology information
Biological speciesPhotorhabdus luminescens (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsBelyy A / Heilen P / Hofnagel O / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2023
Title: Structure and activation mechanism of the Makes caterpillars floppy 1 toxin.
Authors: Alexander Belyy / Philipp Heilen / Philine Hagel / Oliver Hofnagel / Stefan Raunser /
Abstract: The bacterial Makes caterpillars floppy 1 (Mcf1) toxin promotes apoptosis in insects, leading to loss of body turgor and death. The molecular mechanism underlying Mcf1 intoxication is poorly ...The bacterial Makes caterpillars floppy 1 (Mcf1) toxin promotes apoptosis in insects, leading to loss of body turgor and death. The molecular mechanism underlying Mcf1 intoxication is poorly understood. Here, we present the cryo-EM structure of Mcf1 from Photorhabdus luminescens, revealing a seahorse-like shape with a head and tail. While the three head domains contain two effectors, as well as an activator-binding domain (ABD) and an autoprotease, the tail consists of two putative translocation and three putative receptor-binding domains. Rearrangement of the tail moves the C-terminus away from the ABD and allows binding of the host cell ADP-ribosylation factor 3, inducing conformational changes that position the cleavage site closer to the protease. This distinct activation mechanism that is based on a hook-loop interaction results in three autocleavage reactions and the release of two toxic effectors. Unexpectedly, the BH3-like domain containing ABD is not an active effector. Our findings allow us to understand key steps of Mcf1 intoxication at the molecular level.
History
DepositionMay 23, 2023-
Header (metadata) releaseNov 1, 2023-
Map releaseNov 1, 2023-
UpdateDec 27, 2023-
Current statusDec 27, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_17440.png

Downloads & links

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Map

FileDownload / File: emd_17440.map.gz / Format: CCP4 / Size: 236.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationComposite map used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 386 pix.
= 347.4 Å		0.9 Å/pix.
x 410 pix.
= 369. Å		0.9 Å/pix.
x 392 pix.
= 352.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.0017246845 - 0.052279763
Average (Standard dev.)0.000091257265 (±0.0008321852)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-49-53-39
Dimensions410392386
Spacing392410386
CellA: 352.8 Å / B: 369.0 Å / C: 347.4 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: DeepEMhanced composite map

Fileemd_17440_additional_1.map
AnnotationDeepEMhanced composite map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin

EntireName: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
Components
  • Complex: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
    • Protein or peptide: Toxin protein

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Supramolecule #1: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin

SupramoleculeName: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Toxin protein

MacromoleculeName: Toxin protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 329.440219 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH SEQKLISEED LSMASISKDF TNLLNTLIDG QIGAASRQTE WFNMSPDERT DYIKQVDERL QEMQQSTLS VLAAQHFQMQ DNPVSVGDQL QTLQKRRQQM TDVPGTPAIN AYKQQLDRDI LLYRRQQTAM THFDSTWRKV L VMLGPDDS ...String:
MGSSHHHHHH SSGLVPRGSH SEQKLISEED LSMASISKDF TNLLNTLIDG QIGAASRQTE WFNMSPDERT DYIKQVDERL QEMQQSTLS VLAAQHFQMQ DNPVSVGDQL QTLQKRRQQM TDVPGTPAIN AYKQQLDRDI LLYRRQQTAM THFDSTWRKV L VMLGPDDS KPLNATTLRE NAVDKQAKLD TEIKRLEQQL TIQVADSTFS QKYVTLFSEL QAYKDVNARY NALLKASATE EA AALGALT KVPQASDDLP VNISLLMMEE RPGYIRMNVA LVNASTDGRF KDFFLENGRL VVLTDGVLNF SFGTAARSLA WQQ QYRLKS EPPSFRSPTY TPIRSVLVKT EFVEKYFANY LVSESTLRGG FKAQLLGNGR KMLLTSVDRK VPNQIGIQVS GQAP NTTIT REVPLASALS DLINQNADIA SFRTIGLEGF RQSSYHPDRD GLFVNIHELE RSVGFAGRQY LLEMPQDNDY LSATP FGVM SVDGDKVSSS HLSKAQTDTL YQYNAAFFEK LEQLRSGGMK ASRLFEGSIE RTAFVQQLVR LLERNHITPA GVLAPE YPR DNMRDIKGNN LNKVLWEQAF AASVWRSRDN DPLLFRLATR LVKNPAVVKV LQNGYVQSDI AQARELLAPL YEQWRTR AV EAETQRVASA NAAQHPSNPK VHVFDQAEVE RSLDDKLLIL LLTGPQSLEG TDVQLRPMVE AALLSNEGRS LRKQILFH A LRPVADSFSK AAAPVNPHAE LGVGKIMINN RLNQPDPYLI LNTSSEEQAY RDGSYLIKDD KYRSYNQFRP DFKNDATRY MNDLDTPFVG GISGTTQTVS NVLTELFGGA LSVKQYWQFQ MANAAFMIRN GYHSFFETFY VAARYEPEGA DSIGKEMLQM FDKYRVEGS KKALQGKLYD GVMARVLPII NQGLSAADEF HPPRFTRIGP RPALLGQAVK DLELKAGLTS VGDGFEPRQG S ADIHQFVT DPVLFAKTHT VSAEALVRSG RLPAEGSAQL VKVGSGLYEL EYTEQSANDI SSSSIPAYFL GYNGPNQANA VP AYVDIPK RTIAGNFLFT GTLSGGSLVV TSLDANTFRV YHDGRVNSSL LYDNVVMAVD YKDYQIAGTA EGLAAAYMQY VNH EWQLVL QRQEYQRDGQ MLRLRLRDDE EPLSIQVADS QVVERNQAQF VAYREQIHQQ LKKVATQFEV SISGVSDGVY TEGE FSPDH PAIAAWAKLC AEVYDRINAD TKQLVDKRNK LYENRRNTIR RDLINQQIKQ LNITLEYYKA QYDTVLREAG FVEQS WLWQ QIKAKNGSAA VVRIDDTAIQ GGGKQRTDSV GERYAISEAY QRGARGTGFS DGLRNFREIE IPGVDDKMSA LEMKRL FLE GKLTSEQQGA LSGRITETSR AEYIDKVLRQ TAVFSEDFHD AGSVFDRLVP QDFYLSLVGD RSGGRCYPLV RAMTVAL AS GGEAGINSLV QKLFFASADP QAGSSTLLRN SLIKLHSNVE AVQASTELGQ FGLSEVVSRL AATTGTSMFA LNTQNHSM M VGSTVTTEGR RYYFYDPNVG IFAFDNTKSL SRAMEQHLVG RRLAVHYGSF GSKSAPAFNL IEIDTGKMAE VPVGNGLNV ADLTRFEELS SVIGQRRQVE QVMSAQERIT EDLQLSTALQ AFDAEQWGAR FEAASTRLAQ EHQLDSRWLP IIATTEEQGE GRYRVQFIN RDQPEQTRWL DTDDSTFVEF RRFVDEHMSV LNEHFTLESG RMRPRGGVGE AAPVDGLNAG FAVQALIQWF S DKNRHDAA NGMASPDLAT ALKVHSYLNF VQMVHGGVQD VIKVTALVRT ALRGEVVAAQ TSFKEFALSL GHTVNEGVGV LF GGAMIGL DAYELAHAEN DVQKAVFGTQ LAFDSASFVT GAAGIGAGLV GASTAGAVLG GAGVILGGLA VGFTALAQAF GAV AEDAKA VGRYFDTVDK AYKGNGYRYD NEKQVLVPLA GAVIKTLDLS KNQIDFDSQY IYRTHSGSTG SGKINYFFWV GDFP RMVHD RGQAIEVRSG IGYKDVSRPL EHGDSNVVIL PGTPKSYISY EYMLLPGATT RHDAGFDVIR RLEEDKRFDY DFYIF PGEE TIRRIHHEYV DTPIEVVLDQ RNRQLVAPEL PKELHGFLCY EIKGAGGEYL IGLNEGAKVN LTSDVASTWI IDSSQL ASD SISVSKDQLL VGEKGKEVVV KLYLAQNSQV LVVNGKGEVR KVDFTSLTAQ VISEDASKWQ VPGQQIEQHL SDLAKAH QL HGQYVVVENY RHQGRDVGRA FYDVTKDRML FTDTTNEQAK RAQLGAVMGD YAYFYDADNA VAWRVDIATG QVDAQFEP W FNQNAGHISR FWQEGDVVYL ARRYRLKERE AELGYRIIGD RMELVSAVGD DALLQLSARI GRHGDELEAI LQGYRSNST QRGTLMYTLG ARLIQPTSAA LVTVFGVDAA GVPHRYWIRT SDGTLIKPNL APPADQTLHF EAHEQTRSAW QIPADLVLAG SMPLLGGKE VFFFYSKEQK TLFRQEGPGQ EVLDANQPSA LRVTTPALTN VINLNGHLVV VTEDGRVARL DALGQLSYAA V NEHWLKGR IHWWQDLTSV TDGRATLAVF GVKDTDGKSL LPVWYHNGQV VVASAALQDK HPQFLGFEVD GSSARLFEPA SG KLYRQPA MTADALAAAF GTDEVLEASA QLPAANELEP ELHLKAAEQV DAGLRLTTVK GEILLRTHDG KLQLVAVDKD WQQ DNLVRL SQALAEVAGQ WRVKGVLTLQ GDDTQGWFDV GSGQVFSIGG IPATDNLRFI GIAVGKKGAY VYNPTDQMLY QVKE SGAQK LNHYADVERI GSSLLLQDGG KGDLSPMLIA GVDSVVLHGG AGSDTYRLSQ TMWSYYRTVV IDNDDPNQVL DRLII LAVD AEKIFVSRHE DDLMLTDSVN GTVLVIRKVF GSQAVTHRHL QIDLEGSSSV ISVDHLVKGF TRLGTANIGL FELPWA IEL DYKDDDDK

UniProtKB: Toxin 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

BufferpH: 8
GridModel: C-flat-2/1 / Material: COPPER / Mesh: 400
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 2 / Number real images: 21741 / Average electron dose: 70.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 363044
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8p52:
Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin

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