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- PDB-1vom: COMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.... -

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Basic information

Entry
Database: PDB / ID: 1vom
TitleCOMPLEX BETWEEN DICTYOSTELIUM MYOSIN AND MGADP AND VANADATE AT 1.9A RESOLUTION
ComponentsMYOSIN
KeywordsMUSCLE PROTEIN / MYOSIN / MOLECULAR MOTOR / TRANSITION-STATE ANALOG
Function / homology
Function and homology information


uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization ...uropod retraction / cytoplasmic actin-based contraction involved in forward cell motility / phagocytic cup base / pathogen-containing vacuole / response to differentiation-inducing factor 1 / equatorial cell cortex / contractile actin filament bundle assembly / pseudopodium retraction / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / RHO GTPases activate PAKs / adenyl nucleotide binding / calcium-dependent ATPase activity / hypotonic response / actomyosin contractile ring / uropod / apical cortex / detection of mechanical stimulus / negative regulation of actin filament polymerization / actin-myosin filament sliding / substrate-dependent cell migration, cell extension / bleb assembly / actomyosin / filopodium assembly / myosin filament / early phagosome / myosin II complex / cortical actin cytoskeleton organization / cortical actin cytoskeleton / microfilament motor activity / pseudopodium / cleavage furrow / cytoskeletal motor activity / mitotic cytokinesis / response to cAMP / response to mechanical stimulus / 14-3-3 protein binding / extracellular matrix / cell motility / response to hydrogen peroxide / chemotaxis / actin filament binding / intracellular protein localization / regulation of cell shape / cytoplasmic vesicle / cell cortex / cytoskeleton / calmodulin binding / ATP binding / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Alpha-Beta Plaits - #20 / Alpha-Beta Plaits / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain ...Alpha-Beta Plaits - #20 / Alpha-Beta Plaits / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Kinesin / Myosin tail / Myosin tail / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / Other non-globular / Myosin, N-terminal, SH3-like / Myosin N-terminal SH3-like domain profile. / Myosin head, motor domain / Myosin head (motor domain) / Myosin motor domain profile. / Myosin. Large ATPases. / IQ motif profile. / Kinesin motor domain superfamily / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Four Helix Bundle (Hemerythrin (Met), subunit A) / Special / SH3 type barrels. / Roll / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / VANADATE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsRayment, I. / Smith, C.A.
Citation
Journal: Biochemistry / Year: 1996
Title: X-ray structure of the magnesium(II).ADP.vanadate complex of the Dictyostelium discoideum myosin motor domain to 1.9 A resolution.
Authors: Smith, C.A. / Rayment, I.
#1: Journal: Biophys.J. / Year: 1995
Title: Structural Studies of Myosin:Nucleotide Complexes: A Revised Model for the Molecular Basis of Muscle Contraction
Authors: Fisher, A.J. / Smith, C.A. / Thoden, J. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I.
#2: Journal: Biochemistry / Year: 1995
Title: X-Ray Structures of the Myosin Motor Domain of Dictyostelium Discoideum Complexed with Mgadp.Befx and Mgadp.Alf4-
Authors: Fisher, A.J. / Smith, C.A. / Thoden, J.B. / Smith, R. / Sutoh, K. / Holden, H.M. / Rayment, I.
#3: Journal: Science / Year: 1993
Title: Three-Dimensional Structure of Myosin Subfragment-1: A Molecular Motor
Authors: Rayment, I. / Rypniewski, W.R. / Schmidt-Base, K. / Smith, R. / Tomchick, D.R. / Benning, M.M. / Winkelmann, D.A. / Wesenberg, G. / Holden, H.M.
#4: Journal: Biochem.Biophys.Res.Commun. / Year: 1993
Title: Force-Generating Domain of Myosin Motor
Authors: Itakura, S. / Yamakawa, H. / Toyoshima, Y.Y. / Ishijima, A. / Kojima, T. / Harada, Y. / Yanagida, T. / Wakabayashi, T. / Sutoh, K.
History
DepositionNov 9, 1995Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _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_ref_seq_dif.details / _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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,3154
Polymers86,7491
Non-polymers5663
Water12,701705
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)84.500, 145.400, 153.800
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


Mass: 86749.008 Da / Num. of mol.: 1 / Fragment: TRUNCATED AT RESIDUE 762
Source method: isolated from a genetically manipulated source
Details: THIS MOLECULE WAS TRUNCATED TO YIELD A FRAGMENT THAT CRYSTALLIZES READILY
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-VO4 / VANADATE ION


Mass: 114.939 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: VO4
#4: 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 705 / Source method: isolated from a natural source / Formula: H2O
Compound detailsSSBOND THIS LIES BETWEEN TWOFOLD RELATED MOLECULES.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 5.45 Å3/Da / Density % sol: 77.41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12 mMADP11
23 mMsodium vanadate11
31 mM11MgCl2
48.5 %PEG800012
525 mMHEPES12
6250 mM12NaCl
72 mMDTT12
83 %MPD12

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Data collection

Diffraction sourceWavelength: 1.08
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Feb 1, 1995
RadiationScattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionNum. obs: 75066 / % possible obs: 97 % / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.028
Reflection
*PLUS
Highest resolution: 1.9 Å / Num. measured all: 393986

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
RefinementResolution: 1.9→30 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.194 -
all-73626
obs-73626
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 0 33 705 6488
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.012
X-RAY DIFFRACTIONt_angle_deg2.65
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes0.004
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor all: 0.194
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_angle_deg2.656
X-RAY DIFFRACTIONt_dihedral_angle_deg17.32
X-RAY DIFFRACTIONt_plane_restr0.004

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