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- PDB-8br1: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -

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Basic information

Entry
Database: PDB / ID: 8br1
TitleExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MARTX toxin, bound to Latrunculin-B-ATP-Mg-actin, and 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE and 2 Mg ions
Components
  • Actin, alpha skeletal muscle, intermediate form
  • Putative Adenylate cyclase
KeywordsTOXIN / bacterial nucleotidyl cyclase toxin / activated complex
Function / homology
Function and homology information


calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / host cell cytosol / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration ...calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / host cell cytosol / cytoskeletal motor activator activity / myosin heavy chain binding / tropomyosin binding / actin filament bundle / troponin I binding / filamentous actin / mesenchyme migration / actin filament bundle assembly / skeletal muscle myofibril / striated muscle thin filament / skeletal muscle thin filament assembly / actin monomer binding / skeletal muscle fiber development / stress fiber / titin binding / actin filament polymerization / filopodium / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / calcium-dependent protein binding / lamellipodium / transferase activity / cell body / toxin activity / hydrolase activity / protein domain specific binding / cysteine-type endopeptidase activity / calcium ion binding / positive regulation of gene expression / host cell plasma membrane / magnesium ion binding / proteolysis / extracellular region / ATP binding / metal ion binding / identical protein binding / membrane / cytoplasm
Similarity search - Function
Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 ...Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 / 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
3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / ADENOSINE-5'-TRIPHOSPHATE / LATRUNCULIN B / HYDROGEN PEROXIDE / Putative Adenylate cyclase / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesVibrio nigripulchritudo (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.044 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 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
C: Actin, alpha skeletal muscle, intermediate form
B: Putative Adenylate cyclase
D: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)179,47220
Polymers176,2204
Non-polymers3,25216
Water11,674648
1
A: Actin, alpha skeletal muscle, intermediate form
B: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,79911
Polymers88,1102
Non-polymers1,6899
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6660 Å2
ΔGint-67 kcal/mol
Surface area32120 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle, intermediate form
D: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,6739
Polymers88,1102
Non-polymers1,5637
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6020 Å2
ΔGint-65 kcal/mol
Surface area33010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.116, 132.443, 96.396
Angle α, β, γ (deg.)90.000, 110.570, 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 / MARTX toxin


Mass: 46247.477 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio nigripulchritudo (bacteria) / Cell (production host): BL21(DE3) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6N3LUE9, adenylate cyclase

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Non-polymers , 8 types, 664 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
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / 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.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Chemical ChemComp-3AT / 3'-DEOXYADENOSINE-5'-TRIPHOSPHATE / CORDYCEPIN TRIPHOSPHATE


Mass: 491.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O12P3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-PEO / HYDROGEN PEROXIDE


Mass: 34.015 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: H2O2
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 648 / 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: 2.58 Å3/Da / Density % sol: 52.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 26 % peg 3350, 26 % Glycerol, 30 mM LiSO4, 0.1M TrisHCl 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 1 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 26, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 2.044→47.76 Å / Num. obs: 86495 / % possible obs: 84.3 % / Redundancy: 32.7 % / Biso Wilson estimate: 54.49 Å2 / Rmerge(I) obs: 0.162 / Net I/σ(I): 14.1
Reflection shellResolution: 2.044→2.21 Å / Rmerge(I) obs: 3.852 / Num. unique obs: 4319 / % possible all: 28.5

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
AutoProcess1.0.5(20200520)data processing
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
AimlessVersion 0.7.4data scaling
PHASER2.8.3phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PAV

2pav


Resolution: 2.044→47.76 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.94 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.253 / SU Rfree Blow DPI: 0.188 / SU Rfree Cruickshank DPI: 0.19
RfactorNum. reflection% reflectionSelection details
Rfree0.2221 4302 4.97 %RANDOM
Rwork0.19 ---
obs0.1916 86494 76.7 %-
Displacement parametersBiso max: 124.86 Å2 / Biso mean: 61.71 Å2 / Biso min: 35.04 Å2
Baniso -1Baniso -2Baniso -3
1-1.4461 Å20 Å2-0.4354 Å2
2---0.1995 Å20 Å2
3----1.2466 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: final / Resolution: 2.044→47.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11956 0 200 648 12804
Biso mean--52.94 63.7 -
Num. residues----1518
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4362SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2150HARMONIC5
X-RAY DIFFRACTIONt_it12423HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1630SEMIHARMONIC5
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_contact10215SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12423HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16865HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion3.1
X-RAY DIFFRACTIONt_other_torsion17
LS refinement shellResolution: 2.044→2.15 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2405 76 4.39 %
Rwork0.2152 1654 -
obs--10.79 %
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)
10.29950.1916-0.13950.56280.28891.46530.0546-0.0168-0.0033-0.06510.1496-0.0318-0.05760.2156-0.2042-0.0248-0.02960.00350.0183-0.0545-0.03730.358611.186626.2514
20.40190.70940.05342.0179-0.0310.3022-0.00860.04750.02990.1020.09770.10130.003-0.0726-0.08910.00060.0477-0.01890.01120.0616-0.06630.7659-13.507120.1821
30.6262-0.6069-0.22461.24530.38510.74-0.1229-0.05040.07550.01340.2115-0.14370.11780.0943-0.0886-0.04920.0996-0.0154-0.0268-0.0162-0.0083-9.0351-19.492262.5642
40.3978-0.6267-0.13551.3007-0.10950.4258-0.0658-0.0826-0.00860.06150.07380.08010.03020.016-0.00790.00350.02560.0024-0.0060.0259-0.0404-39.95892.699770.6781
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|4 - A|371 }A4 - 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|862 }D466 - 862

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