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- PDB-3ts5: Crystal Structure of a Light Chain Domain of Scallop Smooth Muscl... -

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Basic information

Entry
Database: PDB / ID: 3ts5
TitleCrystal Structure of a Light Chain Domain of Scallop Smooth Muscle Myosin
Components
  • Myosin essential light chain
  • Myosin heavy chain
  • Myosin regulatory light chain
KeywordsSTRUCTURAL PROTEIN / alpha helix / Myosin regulation / Catch muscle
Function / homology
Function and homology information


cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril ...cytoskeletal motor regulator activity / mitotic actomyosin contractile ring / mitotic actomyosin contractile ring contraction / muscle myosin complex / myosin filament / actomyosin structure organization / locomotion / myosin II complex / microfilament motor activity / myofibril / sarcomere organization / myosin heavy chain binding / mitotic cytokinesis / post-embryonic development / muscle contraction / actin filament binding / calcium ion binding / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Myosin, subunit A / Myosin, subunit A / EF-hand 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. ...Myosin, subunit A / Myosin, subunit A / EF-hand 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 / EF-hand / Recoverin; domain 1 / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / Few Secondary Structures / Irregular / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin essential light chain / Myosin regulatory light chain / Myosin heavy chain
Similarity search - Component
Biological speciesPlacopecten magellanicus (sea scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.393 Å
AuthorsKumar, V.S.S. / O'Neall-Hennessey, E. / Reshetnikova, L. / Brown, J.H. / Robinson, H. / Szent-Gyorgyi, A.G. / Cohen, C.
CitationJournal: Biophys.J. / Year: 2011
Title: Crystal structure of a phosphorylated light chain domain of scallop smooth-muscle Myosin.
Authors: Senthil Kumar, V.S. / O'Neall-Hennessey, E. / Reshetnikova, L. / Brown, J.H. / Robinson, H. / Szent-Gyorgyi, A.G. / Cohen, C.
History
DepositionSep 12, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_asym_id / _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.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Myosin heavy chain
B: Myosin regulatory light chain
C: Myosin essential light chain
D: Myosin heavy chain
E: Myosin regulatory light chain
F: Myosin essential light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,49210
Polymers89,3636
Non-polymers1294
Water3,909217
1
A: Myosin heavy chain
B: Myosin regulatory light chain
C: Myosin essential light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7465
Polymers44,6823
Non-polymers642
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8290 Å2
ΔGint-82 kcal/mol
Surface area18990 Å2
MethodPISA
2
D: Myosin heavy chain
E: Myosin regulatory light chain
F: Myosin essential light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7465
Polymers44,6823
Non-polymers642
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8030 Å2
ΔGint-73 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.811, 68.775, 79.418
Angle α, β, γ (deg.)77.33, 85.99, 73.65
Int Tables number1
Space group name H-MP1

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Components

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Protein , 3 types, 6 molecules ADBECF

#1: Protein Myosin heavy chain


Mass: 8598.307 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26080
#2: Protein Myosin regulatory light chain


Mass: 18402.807 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26069
#3: Protein Myosin essential light chain


Mass: 17680.609 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26066

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Non-polymers , 3 types, 221 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 2.91 Å3/Da / Density % sol: 57.69 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 7
Details: 10mM Hepes, 20mM NaCl, 2mM MgCl2, 0.5 mM DTT, 2mM NaN3, 0.2 mM EGTA, 30% MME PEG 2K, 10% MPD, pH 7.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationMonochromator: Sagitally Focusses Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.39→48.753 Å / Num. all: 39386 / Num. obs: 39310 / % possible obs: 99.05 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.39-2.49196.4
2.59-2.71100
3.26-3.581100
3.58-4.11100
4.1-5.171100
5.17-501100

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.393→48.753 Å / SU ML: 0.88 / σ(F): 1.97 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1995 5.08 %
Rwork0.1907 --
obs0.1947 39310 99.05 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 41.933 Å2 / ksol: 0.317 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.4357 Å24.6605 Å2-0.9308 Å2
2--5.0484 Å2-3.1436 Å2
3----2.6127 Å2
Refinement stepCycle: LAST / Resolution: 2.393→48.753 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5924 0 4 217 6145
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0096034
X-RAY DIFFRACTIONf_angle_d1.118088
X-RAY DIFFRACTIONf_dihedral_angle_d17.6032313
X-RAY DIFFRACTIONf_chiral_restr0.08851
X-RAY DIFFRACTIONf_plane_restr0.0041056
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.393-2.45330.33531310.27052455X-RAY DIFFRACTION91
2.4533-2.51970.33471420.25262658X-RAY DIFFRACTION99
2.5197-2.59380.30711440.24052667X-RAY DIFFRACTION100
2.5938-2.67750.28911440.24582713X-RAY DIFFRACTION100
2.6775-2.77320.33411430.24262665X-RAY DIFFRACTION100
2.7732-2.88420.37671430.24862684X-RAY DIFFRACTION100
2.8842-3.01550.32521460.23912718X-RAY DIFFRACTION100
3.0155-3.17440.30671440.22472700X-RAY DIFFRACTION100
3.1744-3.37330.3071430.21962657X-RAY DIFFRACTION100
3.3733-3.63370.26271460.19852727X-RAY DIFFRACTION100
3.6337-3.99920.24831420.17542670X-RAY DIFFRACTION100
3.9992-4.57750.21911420.15042672X-RAY DIFFRACTION99
4.5775-5.76570.18661420.16912649X-RAY DIFFRACTION99
5.7657-48.76340.21251430.16982680X-RAY DIFFRACTION100

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