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- PDB-5t45: Chicken smooth muscle myosin motor domain co-crystallized with th... -

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Basic information

Entry
Database: PDB / ID: 5t45
TitleChicken smooth muscle myosin motor domain co-crystallized with the specific CK-571 inhibitor, MgADP.BeFx form
ComponentsMyosin-11
KeywordsMOTOR PROTEIN / Myosin Inhibitor
Function / homology
Function and homology information


myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / myosin II binding / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development ...myofibril assembly / elastic fiber assembly / myosin light chain binding / skeletal muscle myosin thick filament assembly / myosin II binding / muscle myosin complex / myosin filament / actomyosin structure organization / myosin II complex / cardiac muscle cell development / structural constituent of muscle / microfilament motor activity / myofibril / smooth muscle contraction / ADP binding / actin filament binding / actin binding / calmodulin binding / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain ...DNA repair protein XRCC4-like, C-terminal / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Short calmodulin-binding motif containing conserved Ile and Gln residues. / IQ motif, EF-hand binding site / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-52E / ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Myosin-11
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsSirigu, S. / Planelles-Herrero, V.J. / Hartman, J. / Houdusse, A.
Funding support France, 4items
OrganizationGrant numberCountry
FRM France
French National Research Agency France
AFM France
ARC France
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2016
Title: Highly selective inhibition of myosin motors provides the basis of potential therapeutic application.
Authors: Sirigu, S. / Hartman, J.J. / Planelles-Herrero, V.J. / Ropars, V. / Clancy, S. / Wang, X. / Chuang, G. / Qian, X. / Lu, P.P. / Barrett, E. / Rudolph, K. / Royer, C. / Morgan, B.P. / Stura, E. ...Authors: Sirigu, S. / Hartman, J.J. / Planelles-Herrero, V.J. / Ropars, V. / Clancy, S. / Wang, X. / Chuang, G. / Qian, X. / Lu, P.P. / Barrett, E. / Rudolph, K. / Royer, C. / Morgan, B.P. / Stura, E.A. / Malik, F.I. / Houdusse, A.M.
History
DepositionAug 29, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 16, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2016Group: Database references
Revision 1.2Jan 18, 2017Group: Structure summary
Revision 1.3Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin-11
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,0349
Polymers91,5721
Non-polymers1,4628
Water1,49583
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2400 Å2
ΔGint-15 kcal/mol
Surface area31560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.940, 202.170, 67.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Myosin-11


Mass: 91571.664 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587*PLUS

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Non-polymers , 7 types, 91 molecules

#2: Chemical ChemComp-52E / 4-{[(2-chloro-3-fluorobenzyl)carbamoyl](methyl)amino}-3,4-dideoxy-5-O-(isoquinolin-3-ylcarbamoyl)-D-erythro-pentitol


Mass: 504.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H26ClFN4O5
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-BCN / BICINE


Mass: 163.172 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: pH buffer*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.9 Å3/Da / Density % sol: 57.65 % / Description: Platelet
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.2 / Details: Peg8K, 50 mM Bicine pH 8.2, 10% DMSO

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 25175 / % possible obs: 99.6 % / Redundancy: 7.18 % / Biso Wilson estimate: 72.89 Å2 / Net I/σ(I): 8.88
Reflection shellResolution: 2.8→2.91 Å / % possible all: 99.9

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Processing

Software
NameVersionClassification
BUSTER2.10.2refinement
XDS10.9.4data reduction
XSCALE10.90.4data scaling
PHASER6.4.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BR1

1br1


Resolution: 2.8→44.35 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.881 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.049 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.142 / SU Rfree Blow DPI: 0.36 / SU Rfree Cruickshank DPI: 0.363
RfactorNum. reflection% reflectionSelection details
Rfree0.271 1260 5 %RANDOM
Rwork0.219 ---
obs0.222 25175 99.9 %-
Displacement parametersBiso mean: 64.51 Å2
Baniso -1Baniso -2Baniso -3
1-1.6281 Å20 Å20 Å2
2---8.795 Å20 Å2
3---7.1669 Å2
Refine analyzeLuzzati coordinate error obs: 0.41 Å
Refinement stepCycle: 1 / Resolution: 2.8→44.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5604 0 96 84 5784
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.015823HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.187873HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2063SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes167HARMONIC2
X-RAY DIFFRACTIONt_gen_planes865HARMONIC5
X-RAY DIFFRACTIONt_it5823HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.65
X-RAY DIFFRACTIONt_other_torsion21.47
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion766SEMIHARMONIC5
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_contact6737SEMIHARMONIC4
LS refinement shellResolution: 2.8→2.91 Å / Rfactor Rfree error: 0 / Total num. of bins used: 13
RfactorNum. reflection% reflection
Rfree0.294 141 5 %
Rwork0.226 2677 -
all0.229 2818 -
obs--99.96 %
Refinement TLS params.Method: refined / Origin x: -30.0199 Å / Origin y: 32.977 Å / Origin z: -15.2707 Å
111213212223313233
T-0.2143 Å20.0084 Å2-0.0157 Å2-0.1734 Å2-0.0314 Å2---0.5006 Å2
L1.1726 °20.818 °2-0.251 °2-1.7382 °2-0.4641 °2--0.9129 °2
S0.0687 Å °0.0492 Å °0.009 Å °-0.0347 Å °-0.0569 Å °0.1132 Å °0.1273 Å °-0.0953 Å °-0.0117 Å °
Refinement TLS groupSelection details: { A|* }

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