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- EMDB-17438: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin, t... -

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Basic information

Entry
Database: EMDB / ID: EMD-17438
TitlePhotorhabdus luminescens Makes caterpillars floppy (Mcf) toxin, the tail region of the toxin
Map dataEM density for the bottom part of the protein. It was used to prepare the composite map
Sample
  • Complex: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin
    • Protein or peptide: Makes caterpillars floppy toxin (MCF)
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_17438.png

Downloads & links

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Map

FileDownload / File: emd_17438.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEM density for the bottom part of the protein. It was used to prepare the composite map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 320 pix.
= 288. Å		0.9 Å/pix.
x 320 pix.
= 288. Å		0.9 Å/pix.
x 320 pix.
= 288. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.9 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.006
Minimum - Maximum-0.033214446 - 0.066575766
Average (Standard dev.)0.00006663934 (±0.0009278301)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-160-160-160
Dimensions320320320
Spacing320320320
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: First half-map

Fileemd_17438_half_map_1.map
AnnotationFirst half-map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half-map

Fileemd_17438_half_map_2.map
AnnotationSecond half-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: Makes caterpillars floppy toxin (MCF)

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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: Makes caterpillars floppy toxin (MCF)

MacromoleculeName: Makes caterpillars floppy toxin (MCF) / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH SEQKLISEED LSMASISKDF TNLLNTLIDG QIGAASRQTE WFNMSPDERT DYIKQVDERL QEMQQSTLSV LAAQHFQMQD NPVSVGDQLQ TLQKRRQQMT DVPGTPAINA YKQQLDRDIL LYRRQQTAMT HFDSTWRKVL VMLGPDDSKP ...String:
MGSSHHHHHH SSGLVPRGSH SEQKLISEED LSMASISKDF TNLLNTLIDG QIGAASRQTE WFNMSPDERT DYIKQVDERL QEMQQSTLSV LAAQHFQMQD NPVSVGDQLQ TLQKRRQQMT DVPGTPAINA YKQQLDRDIL LYRRQQTAMT HFDSTWRKVL VMLGPDDSKP LNATTLRENA VDKQAKLDTE IKRLEQQLTI QVADSTFSQK YVTLFSELQA YKDVNARYNA LLKASATEEA AALGALTKVP QASDDLPVNI SLLMMEERPG YIRMNVALVN ASTDGRFKDF FLENGRLVVL TDGVLNFSFG TAARSLAWQQ QYRLKSEPPS FRSPTYTPIR SVLVKTEFVE KYFANYLVSE STLRGGFKAQ LLGNGRKMLL TSVDRKVPNQ IGIQVSGQAP NTTITREVPL ASALSDLINQ NADIASFRTI GLEGFRQSSY HPDRDGLFVN IHELERSVGF AGRQYLLEMP QDNDYLSATP FGVMSVDGDK VSSSHLSKAQ TDTLYQYNAA FFEKLEQLRS GGMKASRLFE GSIERTAFVQ QLVRLLERNH ITPAGVLAPE YPRDNMRDIK GNNLNKVLWE QAFAASVWRS RDNDPLLFRL ATRLVKNPAV VKVLQNGYVQ SDIAQARELL APLYEQWRTR AVEAETQRVA SANAAQHPSN PKVHVFDQAE VERSLDDKLL ILLLTGPQSL EGTDVQLRPM VEAALLSNEG RSLRKQILFH ALRPVADSFS KAAAPVNPHA ELGVGKIMIN NRLNQPDPYL ILNTSSEEQA YRDGSYLIKD DKYRSYNQFR PDFKNDATRY MNDLDTPFVG GISGTTQTVS NVLTELFGGA LSVKQYWQFQ MANAAFMIRN GYHSFFETFY VAARYEPEGA DSIGKEMLQM FDKYRVEGSK KALQGKLYDG VMARVLPIIN QGLSAADEFH PPRFTRIGPR PALLGQAVKD LELKAGLTSV GDGFEPRQGS ADIHQFVTDP VLFAKTHTVS AEALVRSGRL PAEGSAQLVK VGSGLYELEY TEQSANDISS SSIPAYFLGY NGPNQANAVP AYVDIPKRTI AGNFLFTGTL SGGSLVVTSL DANTFRVYHD GRVNSSLLYD NVVMAVDYKD YQIAGTAEGL AAAYMQYVNH EWQLVLQRQE YQRDGQMLRL RLRDDEEPLS IQVADSQVVE RNQAQFVAYR EQIHQQLKKV ATQFEVSISG VSDGVYTEGE FSPDHPAIAA WAKLCAEVYD RINADTKQLV DKRNKLYENR RNTIRRDLIN QQIKQLNITL EYYKAQYDTV LREAGFVEQS WLWQQIKAKN GSAAVVRIDD TAIQGGGKQR TDSVGERYAI SEAYQRGARG TGFSDGLRNF REIEIPGVDD KMSALEMKRL FLEGKLTSEQ QGALSGRITE TSRAEYIDKV LRQTAVFSED FHDAGSVFDR LVPQDFYLSL VGDRSGGRCY PLVRAMTVAL ASGGEAGINS LVQKLFFASA DPQAGSSTLL RNSLIKLHSN VEAVQASTEL GQFGLSEVVS RLAATTGTSM FALNTQNHSM MVGSTVTTEG RRYYFYDPNV GIFAFDNTKS LSRAMEQHLV GRRLAVHYGS FGSKSAPAFN LIEIDTGKMA EVPVGNGLNV ADLTRFEELS SVIGQRRQVE QVMSAQERIT EDLQLSTALQ AFDAEQWGAR FEAASTRLAQ EHQLDSRWLP IIATTEEQGE GRYRVQFINR DQPEQTRWLD TDDSTFVEFR RFVDEHMSVL NEHFTLESGR MRPRGGVGEA APVDGLNAGF AVQALIQWFS DKNRHDAANG MASPDLATAL KVHSYLNFVQ MVHGGVQDVI KVTALVRTAL RGEVVAAQTS FKEFALSLGH TVNEGVGVLF GGAMIGLDAY ELAHAENDVQ KAVFGTQLAF DSASFVTGAA GIGAGLVGAS TAGAVLGGAG VILGGLAVGF TALAQAFGAV AEDAKAVGRY FDTVDKAYKG NGYRYDNEKQ VLVPLAGAVI KTLDLSKNQI DFDSQYIYRT HSGSTGSGKI NYFFWVGDFP RMVHDRGQAI EVRSGIGYKD VSRPLEHGDS NVVILPGTPK SYISYEYMLL PGATTRHDAG FDVIRRLEED KRFDYDFYIF PGEETIRRIH HEYVDTPIEV VLDQRNRQLV APELPKELHG FLCYEIKGAG GEYLIGLNEG AKVNLTSDVA STWIIDSSQL ASDSISVSKD QLLVGEKGKE VVVKLYLAQN SQVLVVNGKG EVRKVDFTSL TAQVISEDAS KWQVPGQQIE QHLSDLAKAH QLHGQYVVVE NYRHQGRDVG RAFYDVTKDR MLFTDTTNEQ AKRAQLGAVM GDYAYFYDAD NAVAWRVDIA TGQVDAQFEP WFNQNAGHIS RFWQEGDVVY LARRYRLKER EAELGYRIIG DRMELVSAVG DDALLQLSAR IGRHGDELEA ILQGYRSNST QRGTLMYTLG ARLIQPTSAA LVTVFGVDAA GVPHRYWIRT SDGTLIKPNL APPADQTLHF EAHEQTRSAW QIPADLVLAG SMPLLGGKEV FFFYSKEQKT LFRQEGPGQE VLDANQPSAL RVTTPALTNV INLNGHLVVV TEDGRVARLD ALGQLSYAAV NEHWLKGRIH WWQDLTSVTD GRATLAVFGV KDTDGKSLLP VWYHNGQVVV ASAALQDKHP QFLGFEVDGS SARLFEPASG KLYRQPAMTA DALAAAFGTD EVLEASAQLP AANELEPELH LKAAEQVDAG LRLTTVKGEI LLRTHDGKLQ LVAVDKDWQQ DNLVRLSQAL AEVAGQWRVK GVLTLQGDDT QGWFDVGSGQ VFSIGGIPAT DNLRFIGIAV GKKGAYVYNP TDQMLYQVKE SGAQKLNHYA DVERIGSSLL LQDGGKGDLS PMLIAGVDSV VLHGGAGSDT YRLSQTMWSY YRTVVIDNDD PNQVLDRLII LAVDAEKIFV SRHEDDLMLT DSVNGTVLVI RKVFGSQAVT HRHLQIDLEG SSSVISVDHL VKGFTRLGTA NIGLFELPWA IELDYKDDDD K

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 reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.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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