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- PDB-8br0: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -

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Basic information

Entry
Database: PDB / ID: 8br0
TitleExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin (residue Q3455 to L3863) in complex with 3'deoxyCTP and two manganese cations bound to Latrunculin-B-ADP-Mn-actin
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 / positive regulation of actin filament polymerization / positive regulation of epithelial cell migration / tropomyosin binding / mesenchyme migration / troponin I binding / myosin heavy chain binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / striated muscle thin filament / actin filament bundle assembly / 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 / RHO GTPases Activate Formins / actin filament / 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 / actin binding / cell cortex / toxin activity / cell body / transferase activity / actin cytoskeleton organization / cytoskeleton / protein stabilization / blood microparticle / 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 / identical protein binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 / : ...Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 / Profilin superfamily / Dermonecrotic/RTX toxin, membrane localization domain / 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 / 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE / LATRUNCULIN B / : / Putative Adenylate cyclase / Profilin-1 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesVibrio nigripulchritudo SFn135 (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.218 Å
AuthorsTexeira-Nuns, M. / Retailleau, P. / Renault, L.
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 22, 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
C: Actin, alpha skeletal muscle, intermediate form
D: Putative Adenylate cyclase,Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)217,10016
Polymers214,1914
Non-polymers2,90912
Water9,746541
1
A: Actin, alpha skeletal muscle, intermediate form
B: Putative Adenylate cyclase,Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5508
Polymers107,0952
Non-polymers1,4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5960 Å2
ΔGint-45 kcal/mol
Surface area31640 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle, intermediate form
D: Putative Adenylate cyclase,Profilin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,5508
Polymers107,0952
Non-polymers1,4556
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5940 Å2
ΔGint-42 kcal/mol
Surface area32510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.469, 132.503, 96.217
Angle α, β, γ (deg.)90.000, 110.400, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ACBD

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


Mass: 41862.613 Da / Num. of mol.: 2 / 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 / Epididymis tissue protein Li 184a / Profilin I


Mass: 65232.859 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio nigripulchritudo SFn135 (bacteria)
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 , 5 types, 553 molecules

#3: Chemical ChemComp-LAB / LATRUNCULIN B


Mass: 395.513 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H29NO5S / Feature type: SUBJECT OF INVESTIGATION / Comment: toxin*YM
#4: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#5: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-CH1 / 3'-DEOXY-CYTIDINE-5'-TRIPHOSPHATE


Mass: 467.157 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H16N3O13P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 541 / 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: 2.63 Å3/Da / Density % sol: 53.18 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 10mg/mL binary complex in the presence of 15.2 mM 3primedCTP1.6 mM ADP, 20 mM MgCl2, 0.2 mM Latrunculin B, 23 mM KCl, 70 mM LiCl, 8 mM HEPES pH 8.5, 4 mM TCEP and mixed with 17 % PEG4000, 17 ...Details: 10mg/mL binary complex in the presence of 15.2 mM 3primedCTP1.6 mM ADP, 20 mM MgCl2, 0.2 mM Latrunculin B, 23 mM KCl, 70 mM LiCl, 8 mM HEPES pH 8.5, 4 mM TCEP and mixed with 17 % PEG4000, 17 % Glycerol, 0.01 M Li2SO4, 0.1 M Tris pH 8.5, 5 mM MgCl2, 15 mM MnCl2, 1% 1-Butyl-2,3-dimethylimidazolium tetrafluoroborate (ionic liquid 18 from the Ionic Liquid Screen (Hampton Research)) in a 1:1.2 v/v hanging drop

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97856 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 22, 2022 / Details: Bimorph Kirkpatrick-Baez mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.218→48.052 Å / Num. obs: 62059 / % possible obs: 92.2 % / Redundancy: 8.4 % / Biso Wilson estimate: 64.232 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.036 / Rrim(I) all: 0.105 / Net I/σ(I): 11.8
Reflection shellResolution: 2.218→2.437 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2919 / CC1/2: 0.59 / Rpim(I) all: 0.471 / % possible all: 49.5

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (3-FEB-2022)refinement
PDB_EXTRACT3.27data extraction
AutoProcess1.0.5data reduction
Aimlessversion 0.7.7data scaling
PHASERv1.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PAV

1pav


Resolution: 2.218→48.05 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.933 / SU R Cruickshank DPI: 0.54 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.527 / SU Rfree Blow DPI: 0.266 / SU Rfree Cruickshank DPI: 0.271
RfactorNum. reflection% reflectionSelection details
Rfree0.2428 2974 4.79 %RANDOM
Rwork0.2085 ---
obs0.2102 62059 71.8 %-
Displacement parametersBiso max: 191.77 Å2 / Biso mean: 72.02 Å2 / Biso min: 28.48 Å2
Baniso -1Baniso -2Baniso -3
1-2.8889 Å20 Å20.2055 Å2
2---1.8311 Å20 Å2
3----1.0578 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: final / Resolution: 2.218→48.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11911 0 170 541 12622
Biso mean--55.97 59.67 -
Num. residues----1515
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4337SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2136HARMONIC5
X-RAY DIFFRACTIONt_it12362HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1628SEMIHARMONIC5
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_contact10314SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12362HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16789HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.03
X-RAY DIFFRACTIONt_other_torsion18.29
LS refinement shellResolution: 2.22→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3747 61 4.91 %
Rwork0.2694 1181 -
all0.2747 1242 -
obs--8.43 %
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)
1-0.01120.1325-0.16770.28530.05060.98270.0316-0.0716-0.0248-0.07090.15970.0391-0.04930.1826-0.19120.0209-0.03780.02060.0251-0.0488-0.054428.959111.871326.2321
20.28510.4373-0.06341.54920.1145-0.08650.0670.04320.02150.087-0.10240.07420.0013-0.02630.03530.0680.0051-0.0148-0.0384-0.0121-0.0580.0703-13.401520.258
30.0919-0.6679-0.20010.81310.18670.4115-0.2227-0.09380.1808-0.06920.1521-0.23050.1972-0.04070.0705-0.03560.1744-0.0388-0.0345-0.03290.0515-9.4524-19.578462.6664
4-0.0453-0.4131-0.01010.71870.11890.3817-0.0088-0.01570.01460.01950.07620.02130.0150.0186-0.06740.0360.06570.0076-0.01570.0014-0.0357-40.02652.959970.4994
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|5 - A|371 }A5 - 371
2X-RAY DIFFRACTION2{ B|466 - B| 863 }B466 - 863
3X-RAY DIFFRACTION3{ C|4 - C|371 }C4 - 371
4X-RAY DIFFRACTION4{ D| 466 - D| 861 }D466 - 861

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