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- EMDB-17435: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin wi... -

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Basic information

Entry
Database: EMDB / ID: EMD-17435
TitlePhotorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3
Map dataPostprocessed map that was used for model building
Sample
  • Complex: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3
    • Complex: Toxin protein
      • Protein or peptide: Toxin protein
    • Complex: ADP-ribosylation factor 3ADP ribosylation factor
      • Protein or peptide: ADP-ribosylation factor 3ADP ribosylation factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION
KeywordsBacterial toxin / Arf / TOXIN
Function / homology
Function and homology information


Synthesis of PIPs at the Golgi membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vesicle-mediated transport / intracellular protein transport / Golgi membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm ...Synthesis of PIPs at the Golgi membrane / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / COPI-dependent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / vesicle-mediated transport / intracellular protein transport / Golgi membrane / GTPase activity / GTP binding / perinuclear region of cytoplasm / extracellular exosome / plasma membrane
Similarity search - Function
ADP-ribosylation factor 1-5 / TcdA/TcdB toxin, pore forming domain / TcdA/TcdB pore forming domain / small GTPase Arf family profile. / Sar1p-like members of the Ras-family of small GTPases / Small GTPase superfamily, ARF/SAR type / ADP-ribosylation factor family / ARF-like small GTPases; ARF, ADP-ribosylation factor / Rab subfamily of small GTPases / Small GTP-binding protein domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
ADP-ribosylation factor 3 / Toxin protein
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 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_17435.png

Downloads & links

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Map

FileDownload / File: emd_17435.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map that was used for model building
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. Å		0.9 Å/pix.
x 300 pix.
= 270. 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: 0.14
Minimum - Maximum-0.44433203 - 1.0567577
Average (Standard dev.)0.0026045567 (±0.030464437)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 270.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_17435_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Second half map

Fileemd_17435_half_map_1.map
AnnotationSecond half map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: First half map

Fileemd_17435_half_map_2.map
AnnotationFirst 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 wi...

EntireName: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3
Components
  • Complex: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3
    • Complex: Toxin protein
      • Protein or peptide: Toxin protein
    • Complex: ADP-ribosylation factor 3ADP ribosylation factor
      • Protein or peptide: ADP-ribosylation factor 3ADP ribosylation factor
  • Ligand: GUANOSINE-5'-TRIPHOSPHATEGuanosine triphosphate
  • Ligand: MAGNESIUM ION

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

SupramoleculeName: Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2

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Supramolecule #2: Toxin protein

SupramoleculeName: Toxin protein / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Supramolecule #3: ADP-ribosylation factor 3

SupramoleculeName: ADP-ribosylation factor 3 / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #2
Source (natural)Organism: Homo sapiens (human)

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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: 325.211562 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGSSHHHHHH SSGLVPRGSH MASISKDFTN LLNTLIDGQI GAASRQTEWF NMSPDERTDY IKQVDERLQE MQQSTLSVLA AQHFQMQDN PVSVGDQLQT LQKRRQQMTD VPGTPAINAY KQQLDRDILL YRRQQTAMTH FDSTWRKVLV MLGPDDSKPL N ATTLRENA ...String:
MGSSHHHHHH SSGLVPRGSH MASISKDFTN LLNTLIDGQI GAASRQTEWF NMSPDERTDY IKQVDERLQE MQQSTLSVLA AQHFQMQDN PVSVGDQLQT LQKRRQQMTD VPGTPAINAY KQQLDRDILL YRRQQTAMTH FDSTWRKVLV MLGPDDSKPL N ATTLRENA VDKQAKLDTE IKRLEQQLTI QVADSTFSQK YVTLFSELQA YKDVNARYNA LLKASATEEA AALGALTKVP QA SDDLPVN ISLLMMEERP GYIRMNVALV NASTDGRFKD FFLENGRLVV LTDGVLNFSF GTAARSLAWQ QQYRLKSEPP SFR SPTYTP IRSVLVKTEF VEKYFANYLV SESTLRGGFK AQLLGNGRKM LLTSVDRKVP NQIGIQVSGQ APNTTITREV PLAS ALSDL INQNADIASF RTIGLEGFRQ SSYHPDRDGL FVNIHELERS VGFAGRQYLL EMPQDNDYLS ATPFGVMSVD GDKVS SSHL SKAQTDTLYQ YNAAFFEKLE QLRSGGMKAS RLFEGSIERT AFVQQLVRLL ERNHITPAGV LAPEYPRDNM RDIKGN NLN KVLWEQAFAA SVWRSRDNDP LLFRLATRLV KNPAVVKVLQ NGYVQSDIAQ ARELLAPLYE QWRTRAVEAE TQRVASA NA AQHPSNPKVH VFDQAEVERS LDDKLLILLL TGPQSLEGTD VQLRPMVEAA LLSNEGRSLR KQILFHALRP VADSFSKA A APVNPHAELG VGKIMINNRL NQPDPYLILN TSSEEQAYRD GSYLIKDDKY RSYNQFRPDF KNDATRYMND LDTPFVGGI SGTTQTVSNV LTELFGGALS VKQYWQFQMA NAAFMIRNGY HSFFETFYVA ARYEPEGADS IGKEMLQMFD KYRVEGSKKA LQGKLYDGV MARVLPIINQ GLSAADEFHP PRFTRIGPRP ALLGQAVKDL ELKAGLTSVG DGFEPRQGSA DIHQFVTDPV L FAKTHTVS AEALVRSGRL PAEGSAQLVK VGSGLYELEY TEQSANDISS SSIPAYFLGY NGPNQANAVP AYVDIPKRTI AG NFLFTGT LSGGSLVVTS LDANTFRVYH DGRVNSSLLY DNVVMAVDYK DYQIAGTAEG LAAAYMQYVN HEWQLVLQRQ EYQ RDGQML RLRLRDDEEP LSIQVADSQV VERNQAQFVA YREQIHQQLK KVATQFEVSI SGVSDGVYTE GEFSPDHPAI AAWA KLCAE VYDRINADTK QLVDKRNKLY ENRRNTIRRD LINQQIKQLN ITLEYYKAQY DTVLREAGFV EQSWLWQQIK AKNGS AAVV RIDDTAIQGG GKQRTDSVGE RYAISEAYQR GARGTGFSDG LRNFREIEIP GVDDKMSALE MKRLFLEGKL TSEQQG ALS GRITETSRAE YIDKVLRQTA VFSEDFHDAG SVFDRLVPQD FYLSLVGDRS GGRAYPLVRA MTVALASGGE AGINSLV QK LFFASADPQA GSSTLLRNSL IKLHSNVEAV QASTELGQFG LSEVVSRLAA TTGTSMFALN TQNHSMMVGS TVTTEGRR Y YFYDPNVGIF AFDNTKSLSR AMEQHLVGRR LAVHYGSFGS KSAPAFNLIE IDTGKMAEVP VGNGLNVADL TRFEELSSV IGQRRQVEQV MSAQERITED LQLSTALQAF DAEQWGARFE AASTRLAQEH QLDSRWLPII ATTEEQGEGR YRVQFINRDQ PEQTRWLDT DDSTFVEFRR FVDEHMSVLN EHFTLESGRM RPRGGVGEAA PVDGLNAGFA VQALIQWFSD KNRHDAANGM A SPDLATAL KVHSYLNFVQ MVHGGVQDVI KVTALVRTAL RGEVVAAQTS FKEFALSLGH TVNEGVGVLF GGAMIGLDAY EL AHAENDV QKAVFGTQLA FDSASFVTGA AGIGAGLVGA STAGAVLGGA GVILGGLAVG FTALAQAFGA VAEDAKAVGR YFD TVDKAY KGNGYRYDNE KQVLVPLAGA VIKTLDLSKN QIDFDSQYIY RTHSGSTGSG KINYFFWVGD FPRMVHDRGQ AIEV RSGIG YKDVSRPLEH GDSNVVILPG TPKSYISYEY MLLPGATTRH DAGFDVIRRL EEDKRFDYDF YIFPGEETIR RIHHE YVDT PIEVVLDQRN RQLVAPELPK ELHGFLCYEI KGAGGEYLIG LNEGAKVNLT SDVASTWIID SSQLASDSIS VSKDQL LVG EKGKEVVVKL YLAQNSQVLV VNGKGEVRKV DFTSLTAQVI SEDASKWQVP GQQIEQHLSD LAKAHQLHGQ YVVVENY RH QGRDVGRAFY DVTKDRMLFT DTTNEQAKRA QLGAVMGDYA YFYDADNAVA WRVDIATGQV DAQFEPWFNQ NAGHISRF W QEGDVVYLAR RYRLKEREAE LGYRIIGDRM ELVSAVGDDA LLQLSARIGR HGDELEAILQ GYRSNSTQRG TLMYTLGAR LIQPTSAALV TVFGVDAAGV PHRYWIRTSD GTLIKPNLAP PADQTLHFEA HEQTRSAWQI PADLVLAGSM PLLGGKEVFF FYSKEQKTL FRQEGPGQEV LDANQPSALR VTTPALTNVI NLNGHLVVVT EDGRVARLDA LGQLSYAAVN EHWLKGRIHW W QDLTSVTD GRATLAVFGV KDTDGKSLLP VWYHNGQVVV ASAALQDKHP QFLGFEVDGS SARLFEPASG KLYRQPAMTA DA LAAAFGT DEVLEASAQL PAANELEPEL HLKAAEQVDA GLRLTTVKGE ILLRTHDGKL QLVAVDKDWQ QDNLVRLSQA LAE VAGQWR VKGVLTLQGD DTQGWFDVGS GQVFSIGGIP ATDNLRFIGI AVGKKGAYVY NPTDQMLYQV KESGAQKLNH YADV ERIGS SLLLQDGGKG DLSPMLIAGV DSVVLHGGAG SDTYRLSQTM WSYYRTVVID NDDPNQVLDR LIILAVDAEK IFVSR HEDD LMLTDSVNGT VLVIRKVFGS QAVTHRHLQI DLEGSSSVIS VDHLVKGFTR

UniProtKB: Toxin protein

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Macromolecule #2: ADP-ribosylation factor 3

MacromoleculeName: ADP-ribosylation factor 3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 20.935895 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MGSSHHHHHH SSGLVPRGSH MRILMVGLDA AGKTTILYKL KLGEIVTTIP TIGFNVETVE YKNISFTVWD VGGLDKIRPL WRHYFQNTQ GLIFVVDSND RERVNEAREE LMRMLAEDEL RDAVLLVFAN KQDLPNAMNA AEITDKLGLH SLRHRNWYIQ A TCATSGDG LYEGLDWLAN QLKNKK

UniProtKB: ADP-ribosylation factor 3

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Macromolecule #3: GUANOSINE-5'-TRIPHOSPHATE

MacromoleculeName: GUANOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 1 / Formula: GTP
Molecular weightTheoretical: 523.18 Da
Chemical component information

ChemComp-GTP:
GUANOSINE-5'-TRIPHOSPHATE / GTP, energy-carrying molecule*YM / Guanosine triphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 18671 / Average electron dose: 62.6 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Startup modelType of model: NONE
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 101942
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6ii6


Chain - Chain ID: C / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-8p50:
Photorhabdus luminescens Makes caterpillars floppy (Mcf) toxin with the C-terminal deletion in complex with Arf3

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