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- PDB-5m05: Chicken smooth muscle myosin motor domain co-crystallized with th... -

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Basic information

Entry
Database: PDB / ID: 5m05
TitleChicken smooth muscle myosin motor domain co-crystallized with the specific CK-571 inhibitor, MgADP 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 / muscle myosin complex / myosin II binding / 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 / muscle myosin complex / myosin II binding / 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. / Myosin head, motor domain / 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. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Chem-52E / ADENOSINE-5'-DIPHOSPHATE / Myosin-11
Similarity search - Component
Biological speciesGallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.675 Å
AuthorsSirigu, S. / 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
DepositionOct 3, 2016Deposition site: PDBE / 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)92,3994
Polymers91,4431
Non-polymers9563
Water97354
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area930 Å2
ΔGint-16 kcal/mol
Surface area32290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.190, 202.970, 67.560
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Myosin-11 / / Myosin heavy chain 11 / Myosin heavy chain / gizzard smooth muscle


Mass: 91442.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: MYH11 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10587
#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-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 2.74 Å3/Da / Density % sol: 55.17 %
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: 0.98011 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 25, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.67→49.68 Å / Num. obs: 29000 / % possible obs: 99 % / Redundancy: 7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 14.23
Reflection shellResolution: 2.67→2.77 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 1.97 / % possible all: 91

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Processing

Software
NameVersionClassification
PHENIX1.8.2_1309refinement
XDS10.9.4data reduction
XSCALE10.90.4data scaling
PHASER6.4.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1BR1

1br1


Resolution: 2.675→49.68 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 2.02 / Phase error: 26.29
RfactorNum. reflection% reflection
Rfree0.244 1451 5 %
Rwork0.1847 --
obs0.1876 28992 98.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.675→49.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5664 0 63 54 5781
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0095833
X-RAY DIFFRACTIONf_angle_d1.2437873
X-RAY DIFFRACTIONf_dihedral_angle_d18.7852190
X-RAY DIFFRACTIONf_chiral_restr0.078869
X-RAY DIFFRACTIONf_plane_restr0.0051015
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6746-2.77020.33851310.25872476X-RAY DIFFRACTION90
2.7702-2.88110.31011450.24592713X-RAY DIFFRACTION100
2.8811-3.01220.32561430.23582754X-RAY DIFFRACTION100
3.0122-3.1710.32591430.23372735X-RAY DIFFRACTION100
3.171-3.36960.28831480.21912749X-RAY DIFFRACTION100
3.3696-3.62970.2721430.19962753X-RAY DIFFRACTION100
3.6297-3.99480.19771480.17622790X-RAY DIFFRACTION100
3.9948-4.57250.22471450.15152793X-RAY DIFFRACTION100
4.5725-5.75950.22181490.16252815X-RAY DIFFRACTION100
5.7595-49.69020.20821560.16692963X-RAY DIFFRACTION100

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