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- EMDB-13160: V. nigripulchritudo ExoY-G-actin-complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13160
TitleV. nigripulchritudo ExoY-G-actin-complex
Map dataDeepEMhanced map
Sample
  • Complex: V. nigripulchritudo ExoY-G-actin-complex
    • Protein or peptide: ExoY
    • Protein or peptide: Actin, alpha skeletal muscle
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / cellular response to cytochalasin B / bBAF complex / npBAF complex / regulation of transepithelial transport / nBAF complex / brahma complex / negative regulation of actin filament polymerization / positive regulation of actin filament bundle assembly / morphogenesis of a polarized epithelium / protein localization to adherens junction / postsynaptic actin cytoskeleton / regulation of actin filament polymerization / structural constituent of postsynaptic actin cytoskeleton / GBAF complex / Formation of annular gap junctions / Signaling by ROBO receptors / Gap junction degradation / regulation of G0 to G1 transition / Tat protein binding / Folding of actin by CCT/TriC / Cell-extracellular matrix interactions / dense body / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / apical protein localization / RSC-type complex / adherens junction assembly / positive regulation of ATP-dependent activity / Adherens junctions interactions / RHOF GTPase cycle / proline-rich region binding / positive regulation of ruffle assembly / PCP/CE pathway / tight junction / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / SWI/SNF complex / Sensory processing of sound by inner hair cells of the cochlea / negative regulation of stress fiber assembly / positive regulation of double-strand break repair / positive regulation of T cell differentiation / host cell cytosol / regulation of norepinephrine uptake / apical junction complex / nitric-oxide synthase binding / positive regulation of actin filament polymerization / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / establishment or maintenance of cell polarity / NuA4 histone acetyltransferase complex / cortical cytoskeleton / positive regulation of stem cell population maintenance / detection of maltose stimulus / maltose transport complex / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of synaptic vesicle endocytosis / regulation of G1/S transition of mitotic cell cycle / Recycling pathway of L1 / brush border / carbohydrate transport / kinesin binding / negative regulation of cell differentiation / actin monomer binding / positive regulation of epithelial cell migration / EPH-ephrin mediated repulsion of cells / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / positive regulation of myoblast differentiation / positive regulation of double-strand break repair via homologous recombination / regulation of protein localization to plasma membrane / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / phosphatidylinositol-4,5-bisphosphate binding / substantia nigra development / calyx of Held / EPHB-mediated forward signaling / phosphotyrosine residue binding / axonogenesis / ATP-binding cassette (ABC) transporter complex / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / adherens junction / positive regulation of cell differentiation / cell chemotaxis / RHO GTPases Activate Formins / FCGR3A-mediated phagocytosis / neural tube closure / cell motility
Similarity search - Function
Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Profilin1/2/3, vertebrate / Dermonecrotic/RTX toxin, membrane localization domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Membrane Localization Domain / Profilin conserved site ...Yersinia/Haemophilus virulence surface antigen / Peptidase C58, YopT-type domain / Profilin1/2/3, vertebrate / Dermonecrotic/RTX toxin, membrane localization domain / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / Membrane Localization Domain / Profilin conserved site / Profilin signature. / Profilin / Profilin / : / Profilin / Profilin superfamily / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / alpha/beta hydrolase fold / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Bacterial extracellular solute-binding protein / Alpha/beta hydrolase fold-1 / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Bacterial extracellular solute-binding protein / Actin / Actin family / Actin / ATPase, nucleotide binding domain / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
RTX-toxin / Profilin-1 / Maltose/maltodextrin-binding periplasmic protein / Actin, cytoplasmic 1
Similarity search - Component
Biological speciesVibrio nigripulchritudo (bacteria) / Oryctolagus cuniculus (rabbit)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsBelyy A / Merino F / Raunser S
Funding support Germany, 1 items
OrganizationGrant numberCountry
Max Planck Society Germany
CitationJournal: Nat Commun / Year: 2021
Title: Mechanism of actin-dependent activation of nucleotidyl cyclase toxins from bacterial human pathogens.
Authors: Alexander Belyy / Felipe Merino / Undine Mechold / Stefan Raunser /
Abstract: Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this ...Bacterial human pathogens secrete initially inactive nucleotidyl cyclases that become potent enzymes by binding to actin inside eukaryotic host cells. The underlying molecular mechanism of this activation is, however, unclear. Here, we report structures of ExoY from Pseudomonas aeruginosa and Vibrio vulnificus bound to their corresponding activators F-actin and profilin-G-actin. The structures reveal that in contrast to the apo-state, two flexible regions become ordered and interact strongly with actin. The specific stabilization of these regions results in an allosteric stabilization of the nucleotide binding pocket and thereby to an activation of the enzyme. Differences in the sequence and conformation of the actin-binding regions are responsible for the selective binding to either F- or G-actin. Other nucleotidyl cyclase toxins that bind to calmodulin rather than actin undergo a similar disordered-to-ordered transition during activation, suggesting that the allosteric activation-by-stabilization mechanism of ExoY is conserved in these enzymes, albeit the different activator.
History
DepositionJul 1, 2021-
Header (metadata) releaseNov 17, 2021-
Map releaseNov 17, 2021-
UpdateDec 1, 2021-
Current statusDec 1, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13160.png

Downloads & links

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Map

FileDownload / File: emd_13160.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationDeepEMhanced map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å		0.85 Å/pix.
x 280 pix.
= 238. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15 / Movie #1: 0.15
Minimum - Maximum-0.0017831661 - 2.4429297
Average (Standard dev.)0.0010925975 (±0.024843154)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions280280280
Spacing280280280
CellA=B=C: 238.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.850.850.85
M x/y/z280280280
origin x/y/z0.0000.0000.000
length x/y/z238.000238.000238.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ300300300
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS280280280
D min/max/mean-0.0022.4430.001

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Supplemental data

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Sample components

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Entire : V. nigripulchritudo ExoY-G-actin-complex

EntireName: V. nigripulchritudo ExoY-G-actin-complex
Components
  • Complex: V. nigripulchritudo ExoY-G-actin-complex
    • Protein or peptide: ExoY
    • Protein or peptide: Actin, alpha skeletal muscle

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Supramolecule #1: V. nigripulchritudo ExoY-G-actin-complex

SupramoleculeName: V. nigripulchritudo ExoY-G-actin-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all

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Macromolecule #1: ExoY

MacromoleculeName: ExoY / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio nigripulchritudo (bacteria)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGYNYGQALQ EAQLDIATMK PRQRVTANEL QLGDDNAITN AVTSEQEATP NQDGSHKTYQ SRDLVLEPIQ HPKSIELGMP EVDQSVLAEV AERENVIIGV RPVDEKSKSL IASKMYSSKG LFVKAKSSDW GPMSGFIPVD QSFAKASARR DLEKFNEYAE QSILSGNAVS ...String:
MGYNYGQALQ EAQLDIATMK PRQRVTANEL QLGDDNAITN AVTSEQEATP NQDGSHKTYQ SRDLVLEPIQ HPKSIELGMP EVDQSVLAEV AERENVIIGV RPVDEKSKSL IASKMYSSKG LFVKAKSSDW GPMSGFIPVD QSFAKASARR DLEKFNEYAE QSILSGNAVS ANLYLNQVRI EELVSKYESL TPLELDVDSG MYKTTATNGD QTIPFFLNKV TVDDKELWQV HYLREGELAP FKVIGDPVSK QPMTADYDLL TVMYTYGDLG PQDKVKQPLT WEQWKESVTY EDLSPKYKAR YDNQALYEKQ DGASLGMVSD RLKELKDVIN TSLGRTDGLE MVHHGADDAN PYAVMADNFP ATFFVPKHFF DDDGLGEGKG SIQTYFNVNE QGAVVIQNPQ EFSNFQQVAI NASYRASLND KWNSGLDSPL FTTKRKLSHD YLDARDEVAK KLGLTESSKL NGLG

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Macromolecule #2: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Oryctolagus cuniculus (rabbit)
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIEHGIITN WDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLDSGD G VTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSSSL EK SYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQK EIT ALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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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: 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 K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 10659 / Average exposure time: 8.0 sec. / Average electron dose: 80.0 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

Particle selectionNumber selected: 1865213
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 236009
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
FSC plot (resolution estimation)

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