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- EMDB-13159: Structure of the V. vulnificus ExoY-G-actin-profilin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-13159
TitleStructure of the V. vulnificus ExoY-G-actin-profilin complex
Map dataMain map, was used to build VvExoY and Actin
Sample
  • Complex: Structure of the V. vulnificus ExoY-G-actin-profilin complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RTX-toxin
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Profilin-1
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / synapse maturation / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex ...calcium- and calmodulin-responsive adenylate cyclase activity / positive regulation of norepinephrine uptake / cellular response to cytochalasin B / synapse maturation / modification of postsynaptic actin cytoskeleton / regulation of transepithelial transport / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / morphogenesis of a polarized epithelium / bBAF complex / postsynaptic actin cytoskeleton organization / protein localization to adherens junction / postsynaptic actin cytoskeleton / npBAF complex / Tat protein binding / brahma complex / structural constituent of postsynaptic actin cytoskeleton / nBAF complex / GBAF complex / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / regulation of G0 to G1 transition / dense body / Formation of annular gap junctions / Gap junction degradation / Signaling by ROBO receptors / Cell-extracellular matrix interactions / Folding of actin by CCT/TriC / regulation of actin filament polymerization / apical protein localization / regulation of double-strand break repair / regulation of nucleotide-excision repair / adherens junction assembly / Prefoldin mediated transfer of substrate to CCT/TriC / RSC-type complex / RHOF GTPase cycle / Adherens junctions interactions / tight junction / positive regulation of ATP-dependent activity / PCP/CE pathway / regulation of norepinephrine uptake / proline-rich region binding / Sensory processing of sound by outer hair cells of the cochlea / positive regulation of ruffle assembly / regulation of mitotic metaphase/anaphase transition / Interaction between L1 and Ankyrins / Sensory processing of sound by inner hair cells of the cochlea / SWI/SNF complex / positive regulation of double-strand break repair / regulation of synaptic vesicle endocytosis / positive regulation of T cell differentiation / negative regulation of stress fiber assembly / host cell cytosol / apical junction complex / establishment or maintenance of cell polarity / regulation of cyclin-dependent protein serine/threonine kinase activity / maintenance of blood-brain barrier / cortical cytoskeleton / detection of maltose stimulus / positive regulation of actin filament polymerization / positive regulation of stem cell population maintenance / NuA4 histone acetyltransferase complex / maltose transport complex / nitric-oxide synthase binding / positive regulation of epithelial cell migration / Recycling pathway of L1 / kinesin binding / regulation of G1/S transition of mitotic cell cycle / carbohydrate transport / brush border / calyx of Held / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / positive regulation of double-strand break repair via homologous recombination / maltose binding / : / actin monomer binding / maltose transport / maltodextrin transmembrane transport / EPH-ephrin mediated repulsion of cells / RHO GTPases Activate WASPs and WAVEs / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of myoblast differentiation / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / EPHB-mediated forward signaling / substantia nigra development / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / ATP-binding cassette (ABC) transporter complex / axonogenesis / cell chemotaxis / negative regulation of protein binding / neural tube closure / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / cell motility / actin filament / positive regulation of cell differentiation / regulation of transmembrane transporter activity
Similarity search - Function
Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Profilin1/2/3, vertebrate / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / : / Profilin conserved site / Profilin signature. ...Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / Profilin1/2/3, vertebrate / Anthrax toxin, edema factor, central / Anthrax toxin, edema factor, C-terminal / Anthrax toxin, edema factor, central domain superfamily / Anthrax toxin LF subunit / : / Profilin conserved site / Profilin signature. / Profilin / Profilin / Profilin / Dermonecrotic/RTX toxin, membrane localization domain / Profilin superfamily / Membrane Localization Domain / Serine aminopeptidase, S33 / CGT/MARTX, cysteine protease (CPD) domain / CGT/MARTX, cysteine protease (CPD) domain superfamily / Peptidase C80 family / CGT/MARTX cysteine protease (CPD) domain profile. / Serine aminopeptidase, S33 / 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. / 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 vulnificus (bacteria) / Homo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 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: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7p1h
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p1h
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13159.png

Downloads & links

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Map

FileDownload / File: emd_13159.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map, was used to build VvExoY and Actin
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.68 Å/pix.
x 320 pix.
= 217.6 Å		0.68 Å/pix.
x 320 pix.
= 217.6 Å		0.68 Å/pix.
x 320 pix.
= 217.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.68 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0025 / Movie #1: 0.0025
Minimum - Maximum-0.004413011 - 0.010719433
Average (Standard dev.)3.19292e-05 (±0.00031533977)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 217.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.680.680.68
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z217.600217.600217.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0040.0110.000

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Supplemental data

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Additional map: Secondary map, was used to build actin-profilin interface

Fileemd_13159_additional_1.map
AnnotationSecondary map, was used to build actin-profilin interface
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 the V. vulnificus ExoY-G-actin-profilin complex

EntireName: Structure of the V. vulnificus ExoY-G-actin-profilin complex
Components
  • Complex: Structure of the V. vulnificus ExoY-G-actin-profilin complex
    • Protein or peptide: Maltose/maltodextrin-binding periplasmic protein,RTX-toxin
    • Protein or peptide: Actin, cytoplasmic 1
    • Protein or peptide: Profilin-1
  • Ligand: CALCIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: Structure of the V. vulnificus ExoY-G-actin-profilin complex

SupramoleculeName: Structure of the V. vulnificus ExoY-G-actin-profilin complex
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3

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Macromolecule #1: Maltose/maltodextrin-binding periplasmic protein,RTX-toxin

MacromoleculeName: Maltose/maltodextrin-binding periplasmic protein,RTX-toxin
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Vibrio vulnificus (bacteria)
Molecular weightTheoretical: 91.467539 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 TNSGSSGSSV EASD TELGT NTDAPHKNYQ SRDLVLEPIV QPETIELGMP DSDQKILAEV AERENVIIGV RPVDEKSKSL IDSKLYSSKG LFVKA KSSD WGPMSGFIPV DQAFAKASAR RDLDKFNGYA EQSIESGNAV SADLYLNQVR IDELVSKYQS LTALEFDAES GMYKTT ATN GDQTVTFFLN KVTVDSKDLW QVHYIKDGKL APFKVIGDPV SKQPMTADYD LLTVMYSYSD LGPQDKLKQP LTWEQWK ES VTYEELTPKY KELYNSEVLY NKKDGASLGV VSDRLKALKD VINTSLGRTD GLEMVHHGAD DANPYAVMAD NFPATFFV P KSFFMEDGLG EGKGSIQTYF NVNEQGAVVI RDPQEFSNFQ QVAINVSYRA SLNDKWNVGL DDPLFTPKSK LSHDFLNAK EEVIKKLSGE VETNVRTTQL LTDNEGL

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Macromolecule #2: Actin, cytoplasmic 1

MacromoleculeName: Actin, cytoplasmic 1 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 41.402242 KDa
Recombinant expressionOrganism: Trichoplusia ni (cabbage looper)
SequenceString: DIAALVVDNG SGMCKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIE(HIC) GIVTNW DDM EKIWHHTFYN ELRVAPEEHP VLLTEAPLNP KANREKMTQI MFETFNTPAM YVAIQAVLSL YASGRTTGIV MDSGDGV TH TVPIYEGYAL ...String:
DIAALVVDNG SGMCKAGFAG DDAPRAVFPS IVGRPRHQGV MVGMGQKDSY VGDEAQSKRG ILTLKYPIE(HIC) GIVTNW DDM EKIWHHTFYN ELRVAPEEHP VLLTEAPLNP KANREKMTQI MFETFNTPAM YVAIQAVLSL YASGRTTGIV MDSGDGV TH TVPIYEGYAL PHAILRLDLA GRDLTDYLMK ILTERGYSFT TTAEREIVRD IKEKLCYVAL DFEQEMATAA SSSSLEKS Y ELPDGQVITI GNERFRCPEA LFQPSFLGME SAGIHETTFN SIMKCDVDIR KDLYANTVLS GGTTMYPGIA DRMQKEITA LAPSTMKIKI IAPPERKYSV WIGGSILASL STFQQMWISK QEYDESGPSI VHRKCF

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Macromolecule #3: Profilin-1

MacromoleculeName: Profilin-1 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.071222 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MAGWNAYIDN LMADGTCQDA AIVGYKDSPS VWAAVPGKTF VNITPAEVGV LVGKDRSSFY VNGLTLGGQK CSVIRDSLLQ DGEFSMDLR TKSTGGAPTF NVTVTKTDKT LVLLMGKEGV HGGLINKKCY EMASHLRRSQ Y

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Macromolecule #4: CALCIUM ION

MacromoleculeName: CALCIUM ION / type: ligand / ID: 4 / Number of copies: 1 / Formula: CA
Molecular weightTheoretical: 40.078 Da

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Macromolecule #5: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 5 / Number of copies: 1 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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 K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Number grids imaged: 1 / Number real images: 6879 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 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: 1.2 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1252333
CTF correctionSoftware - Name: CTFFIND
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPHIRE / Number images used: 342081
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: SPHIRE
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

6nbw

chain_id: A

6nbw

chain_id: C
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-7p1h:
Structure of the V. vulnificus ExoY-G-actin-profilin complex

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