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- EMDB-14532: Structure of P. luminescens TccC3-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-14532
TitleStructure of P. luminescens TccC3-F-actin complex
Map dataThe map was used for building the model
Sample
  • Complex: Structure of P. luminescence TccC3-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,TccC3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: NICOTINAMIDE
Function / homology
Function and homology information


cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / detection of maltose stimulus / actin filament bundle / maltose transport complex / troponin I binding / filamentous actin / mesenchyme migration / carbohydrate transport ...cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / detection of maltose stimulus / actin filament bundle / maltose transport complex / troponin I binding / filamentous actin / mesenchyme migration / carbohydrate transport / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / actin filament / filopodium / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / outer membrane-bounded periplasmic space / cell body / periplasmic space / hydrolase activity / protein domain specific binding / calcium ion binding / DNA damage response / positive regulation of gene expression / magnesium ion binding / ATP binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Toxin complex C-like repeat / Tripartite Tc toxins repeat / Rhs repeat-associated core / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Actins signature 1. / Actin, conserved site ...Toxin complex C-like repeat / Tripartite Tc toxins repeat / Rhs repeat-associated core / : / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Actins signature 1. / Actin, conserved site / Actins signature 2. / Bacterial extracellular solute-binding protein / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Maltose/maltodextrin-binding periplasmic protein / Actin, alpha skeletal muscle / TccC3
Similarity search - Component
Biological speciesPhotorhabdus luminescens (bacteria) / rabbit (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsBelyy A / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2022
Title: Mechanism of threonine ADP-ribosylation of F-actin by a Tc toxin.
Authors: Alexander Belyy / Florian Lindemann / Daniel Roderer / Johanna Funk / Benjamin Bardiaux / Jonas Protze / Peter Bieling / Hartmut Oschkinat / Stefan Raunser /
Abstract: Tc toxins deliver toxic enzymes into host cells by a unique injection mechanism. One of these enzymes is the actin ADP-ribosyltransferase TccC3, whose activity leads to the clustering of the cellular ...Tc toxins deliver toxic enzymes into host cells by a unique injection mechanism. One of these enzymes is the actin ADP-ribosyltransferase TccC3, whose activity leads to the clustering of the cellular cytoskeleton and ultimately cell death. Here, we show in atomic detail how TccC3 modifies actin. We find that the ADP-ribosyltransferase does not bind to G-actin but interacts with two consecutive actin subunits of F-actin. The binding of TccC3 to F-actin occurs via an induced-fit mechanism that facilitates access of NAD to the nucleotide binding pocket. The following nucleophilic substitution reaction results in the transfer of ADP-ribose to threonine-148 of F-actin. We demonstrate that this site-specific modification of F-actin prevents its interaction with depolymerization factors, such as cofilin, which impairs actin network turnover and leads to steady actin polymerization. Our findings reveal in atomic detail a mechanism of action of a bacterial toxin through specific targeting and modification of F-actin.
History
DepositionMar 15, 2022-
Header (metadata) releaseJun 29, 2022-
Map releaseJun 29, 2022-
UpdateMar 15, 2023-
Current statusMar 15, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_14532.png

Downloads & links

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Map

FileDownload / File: emd_14532.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThe map was used for building the model
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: 0.004
Minimum - Maximum-0.006042489 - 0.016007299
Average (Standard dev.)0.0001142701 (±0.00069284224)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 288.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_14532_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_14532_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_14532_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 : Structure of P. luminescence TccC3-F-actin complex

EntireName: Structure of P. luminescence TccC3-F-actin complex
Components
  • Complex: Structure of P. luminescence TccC3-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,TccC3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5-DIPHOSPHORIBOSE
  • Ligand: NICOTINAMIDE

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Supramolecule #1: Structure of P. luminescence TccC3-F-actin complex

SupramoleculeName: Structure of P. luminescence TccC3-F-actin complex / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Photorhabdus luminescens (bacteria)

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: rabbit (rabbit)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Macromolecule #2: Maltose/maltodextrin-binding periplasmic protein,TccC3

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,TccC3
type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Photorhabdus luminescens (bacteria)
Molecular weightTheoretical: 63.658949 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MGSSHHHHHH SSGLVPRGSH MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL ...String:
MGSSHHHHHH SSGLVPRGSH MKIEEGKLVI WINGDKGYNG LAEVGKKFEK DTGIKVTVEH PDKLEEKFPQ VAATGDGPDI IFWAHDRFG GYAQSGLLAE ITPDKAFQDK LYPFTWDAVR YNGKLIAYPI AVEALSLIYN KDLLPNPPKT WEEIPALDKE L KAKGKSAL MFNLQEPYFT WPLIAADGGY AFKYENGKYD IKDVGVDNAG AKAGLTFLVD LIKNKHMNAD TDYSIAEAAF NK GETAMTI NGPWAWSNID TSKVNYGVTV LPTFKGQPSK PFVGVLSAGI NAASPNKELA KEFLENYLLT DEGLEAVNKD KPL GAVALK SYEEELVKDP RIAATMENAQ KGEIMPNIPQ MSAFWYAVRT AVINAASGRQ TVDEALKDAQ TNSGSSGSSG STNL QKKSF TLYRADNRSF EEMQSKFPEG FKAWTPLDTK MARQFASIFI GQKDTSNLPK ETVKNISTWG AKPKLKDLSN YIKYT KDKS TVWVSTAINT EAGGQSSGAP LHKIDMDLYE FAIDGQKLNP LPEGRTKNMV PSLLLDTPQI ETSSIIALNH GPVNDA SIS FLTTIPLKNV KPHKR

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #5: ADENOSINE-5-DIPHOSPHORIBOSE

MacromoleculeName: ADENOSINE-5-DIPHOSPHORIBOSE / type: ligand / ID: 5 / Number of copies: 1 / Formula: APR
Molecular weightTheoretical: 559.316 Da
Chemical component information

ChemComp-APR:
ADENOSINE-5-DIPHOSPHORIBOSE

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Macromolecule #6: NICOTINAMIDE

MacromoleculeName: NICOTINAMIDE / type: ligand / ID: 6 / Number of copies: 1 / Formula: NCA
Molecular weightTheoretical: 122.125 Da
Chemical component information

ChemComp-NCA:
NICOTINAMIDE

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
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: 1 / Number real images: 12284 / Average electron dose: 84.9 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.8000000000000003 µm / Nominal defocus min: 0.4 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2224805
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

5onv

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 437658
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final 3D classificationSoftware - Name: RELION (ver. 3)

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Atomic model buiding 1

Initial modelPDB ID:

5onv

RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7z7h:
Structure of P. luminescens TccC3-F-actin complex

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