[English] 日本語
Yorodumi
- EMDB-13159: Structure of the V. vulnificus ExoY-G-actin-profilin complex -

+
Open data


ID or keywords:

Loading...

-
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
KeywordsBacterial toxin / G-actin / profilin / toxin
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / adenyl-nucleotide exchange factor activity / negative regulation of actin filament bundle assembly / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / positive regulation of actin filament bundle assembly / regulation of actin filament polymerization / Signaling by ROBO receptors / cellular response to cytochalasin B ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / adenyl-nucleotide exchange factor activity / negative regulation of actin filament bundle assembly / modification of postsynaptic actin cytoskeleton / positive regulation of norepinephrine uptake / positive regulation of actin filament bundle assembly / regulation of actin filament polymerization / Signaling by ROBO receptors / cellular response to cytochalasin B / Formation of the embryonic stem cell BAF (esBAF) complex / bBAF complex / npBAF complex / brahma complex / nBAF complex / Formation of the canonical BAF (cBAF) complex / regulation of transepithelial transport / Formation of neuronal progenitor and neuronal BAF (npBAF and nBAF) / morphogenesis of a polarized epithelium / Formation of the polybromo-BAF (pBAF) complex / structural constituent of postsynaptic actin cytoskeleton / Formation of annular gap junctions / Formation of the dystrophin-glycoprotein complex (DGC) / Gap junction degradation / Formation of the non-canonical BAF (ncBAF) complex / GBAF complex / protein localization to adherens junction / regulation of G0 to G1 transition / Cell-extracellular matrix interactions / negative regulation of stress fiber assembly / dense body / Folding of actin by CCT/TriC / Tat protein binding / proline-rich region binding / postsynaptic actin cytoskeleton / RSC-type complex / PCP/CE pathway / Regulation of CDH1 Function / regulation of double-strand break repair / regulation of nucleotide-excision repair / Prefoldin mediated transfer of substrate to CCT/TriC / Adherens junctions interactions / adherens junction assembly / RHOF GTPase cycle / apical protein localization / Sensory processing of sound by outer hair cells of the cochlea / Interaction between L1 and Ankyrins / SWI/SNF complex / regulation of mitotic metaphase/anaphase transition / tight junction / Sensory processing of sound by inner hair cells of the cochlea / positive regulation of T cell differentiation / host cell cytosol / positive regulation of ruffle assembly / apical junction complex / positive regulation of double-strand break repair / detection of maltose stimulus / maintenance of blood-brain barrier / regulation of norepinephrine uptake / transporter regulator activity / positive regulation of stem cell population maintenance / maltose transport complex / NuA4 histone acetyltransferase complex / positive regulation of actin filament polymerization / establishment or maintenance of cell polarity / Recycling pathway of L1 / cortical cytoskeleton / Regulation of MITF-M-dependent genes involved in pigmentation / carbohydrate transport / nitric-oxide synthase binding / positive regulation of epithelial cell migration / brush border / regulation of G1/S transition of mitotic cell cycle / EPH-ephrin mediated repulsion of cells / actin monomer binding / negative regulation of cell differentiation / carbohydrate transmembrane transporter activity / regulation of synaptic vesicle endocytosis / maltose binding / RHO GTPases Activate WASPs and WAVEs / positive regulation of myoblast differentiation / maltose transport / maltodextrin transmembrane transport / kinesin binding / RHO GTPases activate IQGAPs / regulation of protein localization to plasma membrane / positive regulation of double-strand break repair via homologous recombination / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / phosphotyrosine residue binding / phosphatidylinositol-4,5-bisphosphate binding / EPHB-mediated forward signaling / cytoskeleton organization / axonogenesis / substantia nigra development / ATP-binding cassette (ABC) transporter complex / calyx of Held / nitric-oxide synthase regulator activity / FCGR3A-mediated phagocytosis / cell chemotaxis / Translocation of SLC2A4 (GLUT4) to the plasma membrane
Similarity search - Function
Yersinia/Haemophilus virulence surface antigen / Dermonecrotic/RTX toxin, membrane localization domain / Profilin1/2/3, vertebrate / Membrane Localization Domain / Peptidase C58, YopT-type domain / 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 ...Yersinia/Haemophilus virulence surface antigen / Dermonecrotic/RTX toxin, membrane localization domain / Profilin1/2/3, vertebrate / Membrane Localization Domain / Peptidase C58, YopT-type domain / 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 / 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. / alpha/beta hydrolase fold / Maltose/Cyclodextrin ABC transporter, substrate-binding protein / Solute-binding family 1, conserved site / Bacterial extracellular solute-binding proteins, family 1 signature. / Alpha/beta hydrolase fold-1 / 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 / 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
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-
UpdateMar 4, 2026-
Current statusMar 4, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-7p1h
  • Surface level: 0.0025
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-7p1h
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_13159.png

Downloads & links

-
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.)0.0000319292 (±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

-
Supplemental data

-
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)

-
Sample components

-
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

-
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

-
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

UniProtKB: Maltose/maltodextrin-binding periplasmic protein, RTX-toxin

-
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

UniProtKB: Actin, cytoplasmic 1

-
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

UniProtKB: Profilin-1

-
Macromolecule #4: CALCIUM ION

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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 8
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 300
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III

-
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

+
Image processing

Particle selectionNumber selected: 1252333
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
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)

-
Atomic model buiding 1

Initial model
PDB IDChain

6nbw

chain_id: A, source_name: PDB, initial_model_type: experimental model

6nbw

chain_id: C, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more