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- PDB-8bo1: ExoY Nucleotidyl Cyclase domain from Vibrio nigripulchritudo MART... -

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Basic information

Entry
Database: PDB / ID: 8bo1
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 / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle ...calcium- and calmodulin-responsive adenylate cyclase activity / adenylate cyclase / host cell cytosol / cytoskeletal motor activator activity / tropomyosin binding / myosin heavy chain binding / mesenchyme migration / troponin I binding / filamentous actin / actin filament bundle / skeletal muscle thin filament assembly / actin filament bundle assembly / striated muscle thin filament / skeletal muscle myofibril / actin monomer binding / stress fiber / skeletal muscle fiber development / 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 / toxin activity / transferase activity / cell body / 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 / identical protein binding / membrane / metal ion binding / cytoplasm
Similarity search - Function
Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 ...Peptidase C58, YopT-type domain / Yersinia/Haemophilus virulence surface antigen / RtxA toxin / RtxA repeat / 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 / AZIDE ION / LATRUNCULIN B / : / Putative Adenylate cyclase / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesVibrio nigripulchritudo (bacteria)
Oryctolagus cuniculus (rabbit)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.501 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 14, 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
C: Actin, alpha skeletal muscle, intermediate form
D: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)180,20435
Polymers176,2204
Non-polymers3,98431
Water3,891216
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A: Actin, alpha skeletal muscle, intermediate form
B: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,78311
Polymers88,1102
Non-polymers1,6739
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6420 Å2
ΔGint-76 kcal/mol
Surface area31990 Å2
MethodPISA
2
C: Actin, alpha skeletal muscle, intermediate form
D: Putative Adenylate cyclase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)90,42224
Polymers88,1102
Non-polymers2,31222
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-98 kcal/mol
Surface area32170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.500, 132.169, 96.027
Angle α, β, γ (deg.)90.000, 110.800, 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 , 9 types, 247 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-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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#7: 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
#8: Chemical
ChemComp-MN / MANGANESE (II) ION


Mass: 54.938 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Mn / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical
ChemComp-AZI / AZIDE ION


Mass: 42.020 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Formula: N3
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.54 Å3/Da / Density % sol: 51.61 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging 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 2 / Wavelength: 1.8926 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: 1.8926 Å / Relative weight: 1
ReflectionResolution: 2.501→48.24 Å / Num. obs: 45059 / % possible obs: 93.7 % / Redundancy: 28.6 % / CC1/2: 1 / Rmerge(I) obs: 0.154 / Rpim(I) all: 0.029 / Rrim(I) all: 0.157 / Net I/σ(I): 16.2
Reflection shellResolution: 2.501→2.701 Å / Rmerge(I) obs: 4.021 / Mean I/σ(I) obs: 1 / Num. unique obs: 2239 / CC1/2: 0.575 / Rpim(I) all: 0.734 / Rrim(I) all: 4.087

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (20-MAY-2020)refinement
PDB_EXTRACT3.27data extraction
AutoProcess1.0.5 (20200520)data processing
XDSVERSION Feb 5, 2021 BUILT=20210323data reduction
PHASER2.8.3phasing
AimlessVersion 0.7.4data scaling
STARANISOVersion 2.3.36 (11-May-2020)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PAV

2pav


Resolution: 2.501→48.24 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.323
RfactorNum. reflection% reflectionSelection details
Rfree0.2313 2243 4.98 %RANDOM
Rwork0.1906 ---
obs0.1927 45059 74.1 %-
Displacement parametersBiso max: 160.22 Å2 / Biso mean: 85.12 Å2 / Biso min: 41.77 Å2
Baniso -1Baniso -2Baniso -3
1-7.48 Å20 Å22.5153 Å2
2---2.4862 Å20 Å2
3----4.9938 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: final / Resolution: 2.501→48.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11919 0 225 216 12360
Biso mean--76.57 67.63 -
Num. residues----1518
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d4335SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes2146HARMONIC5
X-RAY DIFFRACTIONt_it12397HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion1629SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies5HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact9693SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d12397HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg16829HARMONIC20.98
X-RAY DIFFRACTIONt_omega_torsion2.87
X-RAY DIFFRACTIONt_other_torsion19.59
LS refinement shellResolution: 2.501→2.63 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2829 39 4.32 %
Rwork0.2354 863 -
obs--10.59 %
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)
10.46170.2878-0.4130.97090.44452.56870.0722-0.0529-0.033-0.14460.1296-0.1412-0.09950.23-0.2018-0.0021-0.05630.0557-0.0513-0.0708-0.080629.75411.165525.6525
20.73180.98040.02992.59610.09820.21640.0973-0.01260.06020.2113-0.08950.1669-0.0115-0.1162-0.00770.10740.06320.0208-0.04670.0054-0.15390.3496-13.5820.1052
30.7434-1.0223-0.13921.70670.54741.0742-0.1859-0.08930.2531-0.03090.2043-0.37140.2555-0.0029-0.0184-0.03860.17570.0379-0.1388-0.07120.0265-9.6651-19.718562.4349
40.5491-0.8969-0.08282.0427-0.19020.6123-0.022-0.0080.01510.07210.08810.06270.0827-0.0049-0.06610.05420.03590.0287-0.04430.0077-0.1243-40.3612.83570.0532
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|861 }D466 - 861

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