+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-13160 | |||||||||
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Title | V. nigripulchritudo ExoY-G-actin-complex | |||||||||
Map data | DeepEMhanced map | |||||||||
Sample |
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Function / homology | Function and homology information calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / regulation of transepithelial transport / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / npBAF complex / protein localization to adherens junction / nBAF complex / brahma complex / Tat protein binding / postsynaptic actin cytoskeleton / positive regulation of actin filament bundle assembly / structural constituent of postsynaptic actin cytoskeleton / negative regulation of actin filament polymerization / GBAF complex / Signaling by ROBO receptors / Formation of annular gap junctions / dense body / regulation of G0 to G1 transition / regulation of actin filament polymerization / Gap junction degradation / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / apical protein localization / regulation of double-strand break repair / adherens junction assembly / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / positive regulation of ATP-dependent activity / RHOF GTPase cycle / Adherens junctions interactions / tight junction / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / Interaction between L1 and Ankyrins / Sensory processing of sound by outer hair cells of the cochlea / regulation of mitotic metaphase/anaphase transition / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / regulation of norepinephrine uptake / regulation of synaptic vesicle endocytosis / negative regulation of stress fiber assembly / positive regulation of double-strand break repair / apical junction complex / positive regulation of T cell differentiation / host cell cytosol / positive regulation of actin filament polymerization / regulation of cyclin-dependent protein serine/threonine kinase activity / establishment or maintenance of cell polarity / maintenance of blood-brain barrier / cortical cytoskeleton / NuA4 histone acetyltransferase complex / positive regulation of epithelial cell migration / positive regulation of stem cell population maintenance / detection of maltose stimulus / nitric-oxide synthase binding / maltose transport complex / Regulation of MITF-M-dependent genes involved in pigmentation / regulation of G1/S transition of mitotic cell cycle / maltose binding / carbohydrate transport / Recycling pathway of L1 / brush border / maltose transport / maltodextrin transmembrane transport / kinesin binding / negative regulation of cell differentiation / calyx of Held / actin monomer binding / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / EPH-ephrin mediated repulsion of cells / regulation of protein localization to plasma membrane / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / RHO GTPases activate IQGAPs / phosphatidylinositol-4,5-bisphosphate binding / EPHB-mediated forward signaling / substantia nigra development / phosphotyrosine residue binding / axonogenesis / ATP-binding cassette (ABC) transporter complex / cell chemotaxis / negative regulation of protein binding / neural tube closure / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / cell motility / Translocation of SLC2A4 (GLUT4) to the plasma membrane / actin filament / RHO GTPases Activate Formins / positive regulation of cell differentiation Similarity search - Function | |||||||||
Biological species | Vibrio nigripulchritudo (bacteria) / Oryctolagus cuniculus (rabbit) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Belyy A / Merino F / Raunser S | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_13160.map.gz | 74.1 MB | EMDB map data format | |
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Header (meta data) | emd-13160-v30.xml emd-13160.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_13160_fsc.xml | 10.9 KB | Display | FSC data file |
Images | emd_13160.png | 126.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-13160 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-13160 | HTTPS FTP |
-Validation report
Summary document | emd_13160_validation.pdf.gz | 317.1 KB | Display | EMDB validaton report |
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Full document | emd_13160_full_validation.pdf.gz | 316.6 KB | Display | |
Data in XML | emd_13160_validation.xml.gz | 11 KB | Display | |
Data in CIF | emd_13160_validation.cif.gz | 14.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13160 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-13160 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_13160.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | DeepEMhanced map | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.85 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : V. nigripulchritudo ExoY-G-actin-complex
Entire | Name: V. nigripulchritudo ExoY-G-actin-complex |
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Components |
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-Supramolecule #1: V. nigripulchritudo ExoY-G-actin-complex
Supramolecule | Name: V. nigripulchritudo ExoY-G-actin-complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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-Macromolecule #1: ExoY
Macromolecule | Name: ExoY / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO |
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Source (natural) | Organism: Vibrio nigripulchritudo (bacteria) |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: 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 |
-Macromolecule #2: Actin, alpha skeletal muscle
Macromolecule | Name: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: Oryctolagus cuniculus (rabbit) |
Sequence | String: 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 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 8 |
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Grid | Model: Quantifoil R2/1 / Material: COPPER / Mesh: 300 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination 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 |