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- PDB-1qvi: Crystal structure of scallop myosin S1 in the pre-power stroke st... -

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Basic information

Entry
Database: PDB / ID: 1qvi
TitleCrystal structure of scallop myosin S1 in the pre-power stroke state to 2.6 Angstrom resolution: flexibility and function in the head
Components
  • Myosin essential light chain, striated adductor muscle
  • Myosin heavy chain, striated muscle
  • Myosin regulatory light chain, striated adductor muscle
KeywordsCONTRACTILE PROTEIN / scallop myosin subfragment-1 (S1) / pre-power stroke state / pliant region / internally-uncoupled state / SH1 helix
Function / homology
Function and homology information


cellular component assembly / anatomical structure formation involved in morphogenesis / muscle myosin complex / myosin filament / myosin II complex / myosin complex / microfilament motor activity / myofibril / supramolecular fiber organization / actin filament binding ...cellular component assembly / anatomical structure formation involved in morphogenesis / muscle myosin complex / myosin filament / myosin II complex / myosin complex / microfilament motor activity / myofibril / supramolecular fiber organization / actin filament binding / actin cytoskeleton organization / calmodulin binding / calcium ion binding / ATP binding
Similarity search - Function
Alpha-Beta Plaits - #1590 / Myosin VI head, motor domain, U50 subdomain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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 ...Alpha-Beta Plaits - #1590 / Myosin VI head, motor domain, U50 subdomain / : / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / 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. / 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 / EF-hand / Recoverin; domain 1 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / EF-hand domain pair / Four Helix Bundle (Hemerythrin (Met), subunit A) / 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 / EF-hand domain pair / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin essential light chain, striated adductor muscle / Myosin regulatory light chain, striated adductor muscle / Myosin heavy chain, striated muscle
Similarity search - Component
Biological speciesArgopecten irradians (bay scallop)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.54 Å
AuthorsGourinath, S. / Himmel, D.M. / Brown, J.H. / Reshetnikova, L. / Szent-Gyrgyi, A.G. / Cohen, C.
CitationJournal: Structure / Year: 2003
Title: Crystal structure of scallop Myosin s1 in the pre-power stroke state to 2.6 a resolution: flexibility and function in the head.
Authors: Gourinath, S. / Himmel, D.M. / Brown, J.H. / Reshetnikova, L. / Szent-Gyorgyi, A.G. / Cohen, C.
History
DepositionAug 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 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_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.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_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_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_conn.ptnr2_label_seq_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, striated muscle
Y: Myosin regulatory light chain, striated adductor muscle
Z: Myosin essential light chain, striated adductor muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,6428
Polymers131,0123
Non-polymers6315
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-106 kcal/mol
Surface area51330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.375, 285.623, 59.831
Angle α, β, γ (deg.)90.00, 114.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules AYZ

#1: Protein Myosin heavy chain, striated muscle


Mass: 95815.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P24733
#2: Protein Myosin regulatory light chain, striated adductor muscle / R-LC


Mass: 17560.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P13543
#3: Protein Myosin essential light chain, striated adductor muscle / E-LC / Sulfhydryl light chain / SHLC


Mass: 17635.635 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Argopecten irradians (bay scallop) / References: UniProt: P07291

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Non-polymers , 5 types, 57 molecules

#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#6: 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
#7: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 3

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Sample preparation

CrystalDensity Matthews: 3.05 Å3/Da / Density % sol: 59.64 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: MES, MgCl2, ADP, Na3VO4, polyethylene glycol 8K, glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
140 mMMES1droppH6.0
25 mM1dropMgCl2
330000 nMMgADP1drop
415000 nM1dropNaVO4
56-6.5 %PEG80001drop
63-3.5 %glycerol1drop
780 mM1reservoirNaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 0.93 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 28, 2001
RadiationMonochromator: RH-COATED WITH SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.93 Å / Relative weight: 1
ReflectionResolution: 2.54→50 Å / Num. all: 42849 / Num. obs: 42805 / % possible obs: 82.3 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 48.4 Å2 / Rsym value: 0.083 / Net I/σ(I): 18.6
Reflection shellResolution: 2.55→2.64 Å / Mean I/σ(I) obs: 5 / Num. unique all: 1696 / Rsym value: 0.18 / % possible all: 33
Reflection
*PLUS
Num. obs: 42849 / Rmerge(I) obs: 0.083
Reflection shell
*PLUS
% possible obs: 32.8 % / Rmerge(I) obs: 0.18

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1DFL

1dfl


Resolution: 2.54→45.58 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 2467 5.9 %RANDOM
Rwork0.212 ---
all0.223 42849 --
obs0.212 41515 80.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 28.0872 Å2 / ksol: 0.311881 e/Å3
Displacement parametersBiso mean: 50.9 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å211.15 Å2
2---4.21 Å20 Å2
3---5.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.54→45.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8739 0 35 52 8826
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.6
X-RAY DIFFRACTIONc_improper_angle_d1.44
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.365 131 5.6 %
Rwork0.295 2209 -
obs--26.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2ION.PARAMWATER.TOP
X-RAY DIFFRACTION3WATER.PARAMVD.TOP
X-RAY DIFFRACTION4ADP.PARAMADP.TOP
X-RAY DIFFRACTION5VD.PARAMION.TOP
Refinement
*PLUS
Lowest resolution: 50 Å / % reflection Rfree: 5 % / Rfactor Rwork: 0.211
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg21.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.44
LS refinement shell
*PLUS
% reflection Rfree: 10 %

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