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- PDB-8bji: chimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulch... -

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Basic information

Entry
Database: PDB / ID: 8bji
Titlechimera of ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo fused to a proline-Rich-Domain (PRD) and profilin, bound to ADP-Mg-actin and a sulfate ion
Components
  • Actin, alpha skeletal muscle, intermediate form
  • Putative Adenylate cyclase,Profilin-1
KeywordsTOXIN / bacterial nucleotidyl cyclase toxin / activated complex
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / adenylate cyclase / Signaling by ROBO receptors / regulation of actin filament polymerization ...calcium- and calmodulin-responsive adenylate cyclase activity / synapse maturation / modification of postsynaptic actin cytoskeleton / negative regulation of actin filament bundle assembly / adenyl-nucleotide exchange factor activity / positive regulation of actin filament bundle assembly / negative regulation of actin filament polymerization / adenylate cyclase / Signaling by ROBO receptors / regulation of actin filament polymerization / positive regulation of ATP-dependent activity / PCP/CE pathway / proline-rich region binding / positive regulation of ruffle assembly / negative regulation of stress fiber assembly / host cell cytosol / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / positive regulation of actin filament polymerization / mesenchyme migration / positive regulation of epithelial cell migration / troponin I binding / actin filament bundle / filamentous actin / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / phosphatidylinositol-4,5-bisphosphate binding / actin filament polymerization / phosphotyrosine residue binding / filopodium / neural tube closure / actin filament / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / modulation of chemical synaptic transmission / small GTPase binding / calcium-dependent protein binding / Platelet degranulation / lamellipodium / cell body / actin binding / cell cortex / toxin activity / transferase activity / actin cytoskeleton organization / blood microparticle / protein stabilization / cytoskeleton / hydrolase activity / cadherin binding / protein domain specific binding / cysteine-type endopeptidase activity / focal adhesion / glutamatergic synapse / calcium ion binding / positive regulation of gene expression / regulation of transcription by RNA polymerase II / host cell plasma membrane / magnesium ion binding / proteolysis / RNA binding / extracellular exosome / extracellular region / ATP binding / membrane / identical protein binding / metal ion binding / nucleus / cytosol / cytoplasm
Similarity search - Function
RtxA toxin / RtxA repeat / 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 / : ...RtxA toxin / RtxA repeat / 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 / 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'-DIPHOSPHATE / DI(HYDROXYETHYL)ETHER / HYDROGEN PEROXIDE / Putative Adenylate cyclase / Profilin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesVibrio nigripulchritudo (bacteria)
Homo sapiens (human)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTeixeira-Nunes, M. / Renault, L. / Retailleau, P.
Funding support France, 1items
OrganizationGrant numberCountry
Agence Nationale de la Recherche (ANR)ANR-18-CE44-0004 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
B: Putative Adenylate cyclase,Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,13629
Polymers107,0952
Non-polymers2,04127
Water17,006944
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)81.974, 62.854, 93.588
Angle α, β, γ (deg.)90.000, 90.280, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 2 molecules AB

#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 Putative Adenylate cyclase,Profilin-1 / MARTX toxin / Epididymis tissue protein Li 184a / Profilin I


Mass: 65232.859 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera containing ExoY nucleotidyl cyclase domain from Vibrio nigripulchritudo MARTX (amino-acids 4 to 446), fused to a Proline-Rich-Motif (amino-acids 447 to 450) and human profilin 1 ...Details: chimera containing ExoY nucleotidyl cyclase domain from Vibrio nigripulchritudo MARTX (amino-acids 4 to 446), fused to a Proline-Rich-Motif (amino-acids 447 to 450) and human profilin 1 (amino-acids 453 to 591, Uniprot: P07737)
Source: (gene. exp.) Vibrio nigripulchritudo (bacteria), (gene. exp.) Homo sapiens (human)
Gene: VIBNISFn135_p10220, PFN1 / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli)
References: UniProt: A0A6N3LUE9, UniProt: P07737, adenylate cyclase

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Non-polymers , 8 types, 971 molecules

#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#6: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#8: Chemical
ChemComp-PEO / HYDROGEN PEROXIDE / Hydrogen peroxide


Mass: 34.015 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: H2O2
#9: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 944 / 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: 2.25 Å3/Da / Density % sol: 45.36 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 8.5
Details: 30% peg 4000, 0.2 M Lithium Sulfate (LiSO4), 0.1 M TrisHCl pH8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.979 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 3, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.64→61.81 Å / Num. obs: 83837 / % possible obs: 94.6 % / Redundancy: 7 % / Biso Wilson estimate: 26 Å2 / Rmerge(I) obs: 0.123 / Net I/σ(I): 8.5
Reflection shellResolution: 1.64→1.82 Å / Rmerge(I) obs: 1.094 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 4192

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
AutoProcess1.0.5 (20200206)data processing
XDSVersion Jan 31, 2020 BUILT=20200131data reduction
AimlessVersion 0.7.4data scaling
STARANISOVersion 2.3.24 (29-Jan-2020)data scaling
PHASERVersion 2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PAV

2pav


Resolution: 1.75→25.06 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU R Cruickshank DPI: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.138 / SU Rfree Blow DPI: 0.126 / SU Rfree Cruickshank DPI: 0.121
RfactorNum. reflection% reflectionSelection details
Rfree0.2121 4141 5.04 %RANDOM
Rwork0.1753 ---
obs0.1772 82105 85.4 %-
Displacement parametersBiso max: 92.73 Å2 / Biso mean: 30.28 Å2 / Biso min: 12.03 Å2
Baniso -1Baniso -2Baniso -3
1-0.0937 Å20 Å20.4811 Å2
2--0.171 Å20 Å2
3----0.2647 Å2
Refine analyzeLuzzati coordinate error obs: 0.22 Å
Refinement stepCycle: final / Resolution: 1.75→25.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6726 0 125 944 7795
Biso mean--42.05 38.89 -
Num. residues----864
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2506SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1234HARMONIC5
X-RAY DIFFRACTIONt_it7126HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion929SEMIHARMONIC5
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_contact7067SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7126HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg9661HARMONIC20.92
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion15.83
LS refinement shellResolution: 1.75→1.8 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.2688 70 4.26 %
Rwork0.2246 1573 -
all0.2267 1643 -
obs--22.2 %
Refinement TLS params.Method: refined / Origin x: 26.3109 Å / Origin y: 0.1767 Å / Origin z: 11.3893 Å
111213212223313233
T-0.0036 Å2-0.0091 Å20.0082 Å2--0.0182 Å2-0.0113 Å2---0.0058 Å2
L0.0497 °2-0.0253 °20.0974 °2-0.0048 °20.0096 °2--0.3795 °2
S-0.0085 Å °0.0078 Å °0.0144 Å °0.0017 Å °-0.0069 Å °-0.0184 Å °-0.0044 Å °-0.0251 Å °0.0154 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A | * }
2X-RAY DIFFRACTION1{ B | * }

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