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- PDB-6r5m: Crystal structure of toxin MT9 from mamba venom -

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Basic information

Entry
Database: PDB / ID: 6r5m
TitleCrystal structure of toxin MT9 from mamba venom
ComponentsDendroaspis polylepis MT9
KeywordsTOXIN / mamba venom / aminergic toxin
Function / homology
Function and homology information


toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / CD59 / CD59 / Ribbon / Mainly Beta
Similarity search - Domain/homology
ACETYL GROUP / S-1,2-PROPANEDIOL / Dendroaspis polylepis MT9
Similarity search - Component
Biological speciesDendroaspis polylepis (cobra)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsStura, E.A. / Tepshi, L. / Ciolek, J. / Triquigneaux, M. / Zoukimian, C. / De Waard, M. / Beroud, R. / Servent, D. / Gilles, N. / Legrand, P. / Ciccone, L.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-11-RPIB-022-04 venompicoscreen France
CitationJournal: Biomed Pharmacother / Year: 2022
Title: MT9, a natural peptide from black mamba venom antagonizes the muscarinic type 2 receptor and reverses the M2R-agonist-induced relaxation in rat and human arteries
Authors: Ciolek, J. / Zoukimian, C. / Dhot, J. / Burban, M. / Triquigneaux, M. / Lauzier, B. / Guimbert, C. / Boturyn, D. / Ferron, M. / Ciccone, L. / Tepshi, L. / Stura, E. / Legrand, P. / Robin, P. ...Authors: Ciolek, J. / Zoukimian, C. / Dhot, J. / Burban, M. / Triquigneaux, M. / Lauzier, B. / Guimbert, C. / Boturyn, D. / Ferron, M. / Ciccone, L. / Tepshi, L. / Stura, E. / Legrand, P. / Robin, P. / Mourier, G. / Schaack, B. / Fellah, I. / Blanchet, G. / Gauthier-Erfanian, C. / Beroud, R. / Servent, D. / De Waard, M. / Gilles, N.
History
DepositionMar 25, 2019Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 12, 2020ID: 6F21
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1May 25, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dendroaspis polylepis MT9
B: Dendroaspis polylepis MT9
C: Dendroaspis polylepis MT9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,27616
Polymers19,1233
Non-polymers1,15313
Water2,792155
1
A: Dendroaspis polylepis MT9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,7195
Polymers6,3741
Non-polymers3444
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dendroaspis polylepis MT9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,6594
Polymers6,3741
Non-polymers2843
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Dendroaspis polylepis MT9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,8997
Polymers6,3741
Non-polymers5246
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)69.550, 93.640, 62.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-102-

SO4

21C-220-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Dendroaspis polylepis MT9


Mass: 6374.473 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Dendroaspis polylepis (cobra) / References: UniProt: A0A4P1LYC9*PLUS

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Non-polymers , 5 types, 168 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-PGO / S-1,2-PROPANEDIOL


Mass: 76.094 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C3H8O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ACE / ACETYL GROUP


Mass: 44.053 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H4O
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / Source method: isolated from a natural source / Formula: H2O

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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: 2.65 Å3/Da / Density % sol: 53.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.05 M A.S 0.06 M sodium citrate, pH 5.5 with 35 mM NaSCN.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.980097 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Sep 20, 2017 / Details: KB Mirrors
RadiationMonochromator: [111]Si Cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.980097 Å / Relative weight: 1
ReflectionResolution: 1.9→47 Å / Num. obs: 16308 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6 % / Biso Wilson estimate: 34.42 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.177 / Rpim(I) all: 0.078 / Rrim(I) all: 0.199 / Net I/σ(I): 6.6
Reflection shellHighest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→19.45 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.909 / SU R Cruickshank DPI: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.192 / SU Rfree Blow DPI: 0.156 / SU Rfree Cruickshank DPI: 0.146
RfactorNum. reflection% reflectionSelection details
Rfree0.251 813 4.99 %RANDOM
Rwork0.231 ---
obs0.232 16290 99.6 %-
Displacement parametersBiso mean: 40.18 Å2
Baniso -1Baniso -2Baniso -3
1--0.3759 Å20 Å20 Å2
2---6.944 Å20 Å2
3---7.3199 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å
Refinement stepCycle: LAST / Resolution: 1.9→19.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1314 0 64 155 1533
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0081422HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.131922HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d498SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes228HARMONIC5
X-RAY DIFFRACTIONt_it1422HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.14
X-RAY DIFFRACTIONt_other_torsion15.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion188SEMIHARMONIC5
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_contact1706SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.92 Å / Total num. of bins used: 40
RfactorNum. reflection% reflection
Rfree0.3805 -4.9 %
Rwork0.3258 388 -
all0.3283 408 -
obs--95.74 %
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)
13.3588-0.8352-0.56981.78610.09644.4385-0.0626-0.11390.0994-0.10040.06290.0118-0.4547-0.0944-0.00030.02910.0413-0.0015-0.0727-0.01130.0242-8.24524.625526.1374
20.61340.02690.67474.25181.75173.91370.0448-0.0025-0.0623-0.4136-0.0507-0.03880.09260.22570.006-0.0014-0.00250.0201-0.0122-0.0077-0.01294.33378.208418.7235
35.3306-1.80421.60091.97910.2694.00110.03390.45570.0286-0.0142-0.10.0804-0.021-0.04630.06620.11450.06960.002-0.01610.0272-0.052-10.77717.08451.2508
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }

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