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- PDB-8bjj: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -

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Basic information

Entry
Database: PDB / ID: 8bjj
TitleExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to ATP-Mg-actin, human profilin 1 and a sulfate ion
Components
  • Actin, alpha skeletal muscle, intermediate form
  • Profilin-1
  • Putative Adenylate cyclase
KeywordsTOXIN / bacterial nucleotidyl cyclase toxin / activated complex
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / adenylate cyclase / regulation of actin filament polymerization / Signaling by ROBO receptors ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / adenyl-nucleotide exchange factor activity / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / adenylate cyclase / regulation of actin filament polymerization / Signaling by ROBO receptors / positive regulation of ATP-dependent activity / proline-rich region binding / PCP/CE pathway / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / cytoskeletal motor activator activity / host cell cytosol / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / positive regulation of actin filament polymerization / mesenchyme migration / skeletal muscle myofibril / actin filament bundle assembly / striated muscle thin filament / skeletal muscle thin filament assembly / positive regulation of epithelial cell migration / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / phosphotyrosine residue binding / actin filament polymerization / neural tube closure / filopodium / actin filament / RHO GTPases Activate Formins / modulation of chemical synaptic transmission / small GTPase binding / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / Platelet degranulation / lamellipodium / transferase activity / toxin activity / cell body / actin binding / actin cytoskeleton organization / cell cortex / blood microparticle / cytoskeleton / protein stabilization / hydrolase activity / cadherin binding / protein domain specific binding / cysteine-type endopeptidase activity / focal adhesion / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / host cell plasma membrane / glutamatergic synapse / magnesium ion binding / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / metal ion binding / identical protein binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / Profilin1/2/3, vertebrate / Peptidase C58, YopT-type domain / 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 ...Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / Profilin1/2/3, vertebrate / Peptidase C58, YopT-type domain / 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. / Serralysin-like metalloprotease, C-terminal / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / ATPase, nucleotide binding domain
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / HYDROGEN PEROXIDE / Putative Adenylate cyclase / Profilin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
Vibrio nigripulchritudo (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.699 Å
AuthorsTeixeira-Nunes, M. / Renault, L. / Retailleau, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0001 France
CitationJournal: Plos Pathog. / Year: 2023
Title: Functional and structural insights into the multi-step activation and catalytic mechanism of bacterial ExoY nucleotidyl cyclase toxins bound to actin-profilin.
Authors: Teixeira-Nunes, M. / Retailleau, P. / Raoux-Barbot, D. / Comisso, M. / Missinou, A.A. / Velours, C. / Plancqueel, S. / Ladant, D. / Mechold, U. / Renault, L.
History
DepositionNov 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 20, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Actin, alpha skeletal muscle, intermediate form
C: Profilin-1
B: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,96016
Polymers103,0503
Non-polymers1,91013
Water13,007722
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.186, 63.202, 93.455
Angle α, β, γ (deg.)90.000, 91.040, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ACB

#1: Protein Actin, alpha skeletal muscle, intermediate form


Mass: 41862.613 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: skeletal muscle / References: UniProt: P68135
#2: Protein Profilin-1 / Epididymis tissue protein Li 184a / Profilin I


Mass: 14940.021 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PFN1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P07737
#3: Protein Putative Adenylate cyclase / MARTX toxin


Mass: 46247.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio nigripulchritudo (bacteria) / Cell (production host): BL21(DE3) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6N3LUE9, adenylate cyclase

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Non-polymers , 9 types, 735 molecules

#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H29NO5S / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#8: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H2O2
#10: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 722 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.88 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 8.5 / Details: 30% peg3000 0.3M LiSO4 0.1M Tris pH8.5 3% Dioxane

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.699→44.2 Å / Num. obs: 104207 / % possible obs: 99.8 % / Redundancy: 15.2 % / Biso Wilson estimate: 27.04 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 25.3
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.055 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 5211

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
AutoProcess1.0.5 (20200520)data processing
XDSVERSION Jan 31, 2020 BUILT=20200417data reduction
Aimlessversion 0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PAV

2pav


Resolution: 1.699→44.2 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.954 / SU R Cruickshank DPI: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.1 / SU Rfree Blow DPI: 0.092 / SU Rfree Cruickshank DPI: 0.09
RfactorNum. reflection% reflectionSelection details
Rfree0.1949 5186 4.98 %RANDOM
Rwork0.1751 ---
obs0.1761 104207 99.8 %-
Displacement parametersBiso max: 110.7 Å2 / Biso mean: 33.36 Å2 / Biso min: 11.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.2029 Å20 Å20.7063 Å2
2--1.0191 Å20 Å2
3----0.8162 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å
Refinement stepCycle: final / Resolution: 1.699→44.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6718 0 118 723 7559
Biso mean--34.68 40.8 -
Num. residues----861
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2598SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1275HARMONIC5
X-RAY DIFFRACTIONt_it7210HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion947SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7010SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7210HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9816HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion3.34
X-RAY DIFFRACTIONt_other_torsion15.95
LS refinement shellResolution: 1.7→1.71 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2376 97 4.65 %
Rwork0.2253 1988 -
all0.2258 2085 -
obs--96.43 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.46980.08490.16420.0561-0.00560.4178-0.02740.0569-0.0372-0.01950.0013-0.05210.0193-0.05350.0262-0.0048-0.01320.0230.0032-0.0221-0.013326.0598-7.563523.1738
20.06310.11370.10260.04820.01571.2473-0.05520.017-0.02770.0299-0.0577-0.05910.0034-0.11060.1130.00710.0338-0.00350.00230.0102-0.035416.93645.9828-14.6297
30.4044-0.3241-0.40310.76720.64731.4256-0.0299-0.09130.09150.0480.1596-0.25240.0270.1343-0.1297-0.01940.0033-0.0338-0.0324-0.04790.078647.99054.992746.8696
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|375 }A5 - 375
2X-RAY DIFFRACTION2{ B|466 - B|863 }B466 - 863
3X-RAY DIFFRACTION3{ C|1 - C|139 }C1 - 139

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