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Basic information

Entry
Database: PDB / ID: 3pn7
TitleVisualizing new hinges and a potential major source of compliance in the lever arm of myosin
Components
  • Myosin essential light chain
  • Myosin heavy chain
  • Myosin regulatory light chain
KeywordsPROTEIN BINDING / alpha helix / muscle contraction / Calcium binding / 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: 2.25 Å
AuthorsBrown, J.H. / Senthil-Kumar, V.S. / O'Neall-Hennessey, E. / Reshetnikova, L. / Robinson, H. / Nguyen-McCarty, M. / Szent-Gyorgyi, A.G. / Cohen, C.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Visualizing key hinges and a potential major source of compliance in the lever arm of myosin.
Authors: Brown, J.H. / Senthil Kumar, V.S. / O'Neall-Hennessey, E. / Reshetnikova, L. / Robinson, H. / Nguyen-McCarty, M. / Szent-Gyorgyi, A.G. / Cohen, C.
History
DepositionNov 18, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 5, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: 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 / 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
Water8,827490
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 area8120 Å2
ΔGint-61 kcal/mol
Surface area19040 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 area8020 Å2
ΔGint-73 kcal/mol
Surface area19270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.737, 68.779, 79.305
Angle α, β, γ (deg.)77.41, 85.94, 73.61
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 / Details: muscle / 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 / Details: Muscle / 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 / Details: muscle / Source: (natural) Placopecten magellanicus (sea scallop) / References: UniProt: Q26066

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Non-polymers , 3 types, 494 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.: 490 / 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: 57.58 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 7
Details: 1.1-1.6 mg/ml protein in 5mM HEPES buffer, 20mM NaCl, 1.5mM MgCl2, 0.5-1mM CaCl2, 0.1mM EGTA, 0.5mM DTT, 2mM NaN3, 0.5 ug/ml leupeptin, 0.7 ug/ml pepstatin-A and 7.5% (w/v) of polyethylene ...Details: 1.1-1.6 mg/ml protein in 5mM HEPES buffer, 20mM NaCl, 1.5mM MgCl2, 0.5-1mM CaCl2, 0.1mM EGTA, 0.5mM DTT, 2mM NaN3, 0.5 ug/ml leupeptin, 0.7 ug/ml pepstatin-A and 7.5% (w/v) of polyethylene glycol 3350 (PEG 3350) or polyethylene glycol monomethyl ether 2000 (MME PEG 2K). The reservoir solution: 10 mM HEPES, 40mM NaCl, 3 mM MgCl2, 2 mM NaN3 and 15% PEG 3350 or MME, PEG 2K, pH 7.0, VAPOR DIFFUSION, temperature 277K

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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 / Date: Nov 3, 2009
RadiationMonochromator: Sagitally Focussed Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 46183 / % possible obs: 96.2 % / Observed criterion σ(F): 3 / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 16.9
Reflection shellResolution: 2.24→2.33 Å / % possible all: 82

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
PHENIX(phenix.refine: 2009_12_14_1757)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WDC

1wdc


Resolution: 2.25→48.672 Å / SU ML: 0.31 / σ(F): 0.12 / Phase error: 25.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2414 1904 4.2 %
Rwork0.1913 --
obs0.1913 45375 95.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.564 Å2 / ksol: 0.324 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--2.8352 Å23.44 Å2-1.4863 Å2
2--5.9959 Å2-1.5486 Å2
3----3.1607 Å2
Refinement stepCycle: LAST / Resolution: 2.25→48.672 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5913 0 4 490 6407
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086021
X-RAY DIFFRACTIONf_angle_d1.0998069
X-RAY DIFFRACTIONf_dihedral_angle_d16.9542312
X-RAY DIFFRACTIONf_chiral_restr0.079847
X-RAY DIFFRACTIONf_plane_restr0.0051054
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.25-2.30610.32041250.25082751X-RAY DIFFRACTION83
2.3061-2.36850.29741200.22532849X-RAY DIFFRACTION88
2.3685-2.43820.3031300.22252995X-RAY DIFFRACTION91
2.4382-2.51690.30221290.21633050X-RAY DIFFRACTION93
2.5169-2.60680.2931350.21633063X-RAY DIFFRACTION95
2.6068-2.71120.29431360.20633099X-RAY DIFFRACTION95
2.7112-2.83460.26231360.21293157X-RAY DIFFRACTION96
2.8346-2.9840.29491370.22083136X-RAY DIFFRACTION97
2.984-3.17090.28811410.21253189X-RAY DIFFRACTION97
3.1709-3.41570.26261430.20813209X-RAY DIFFRACTION99
3.4157-3.75930.2431420.18213245X-RAY DIFFRACTION100
3.7593-4.3030.19491440.16023254X-RAY DIFFRACTION100
4.303-5.42020.21311420.15463227X-RAY DIFFRACTION100
5.4202-48.68350.18411440.16523247X-RAY DIFFRACTION99

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