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- PDB-1mmd: TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED ... -

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Basic information

Entry
Database: PDB / ID: 1mmd
TitleTRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM COMPLEXED WITH MGADP-BEF3
ComponentsMYOSIN
KeywordsCONTRACTILE PROTEIN / ATPASE / MYOSIN / COILED COIL / ACTIN-BINDING / ATP-BINDING / HEPTAD REPEAT PATTERN / METHYLATION / ALKYLATION / PHOSPHORYLATION
Function / homology
Function and homology information


calcium-dependent ATPase activity / RHO GTPases activate PAKs / pseudopodium retraction / equatorial cell cortex / uropod retraction / response to differentiation-inducing factor 1 / phagocytic cup base / cytoplasmic actin-based contraction involved in forward cell motility / contractile actin filament bundle assembly / cell trailing edge ...calcium-dependent ATPase activity / RHO GTPases activate PAKs / pseudopodium retraction / equatorial cell cortex / uropod retraction / response to differentiation-inducing factor 1 / phagocytic cup base / cytoplasmic actin-based contraction involved in forward cell motility / contractile actin filament bundle assembly / cell trailing edge / contractile vacuole organization / myosin filament assembly / aggregation involved in sorocarp development / culmination involved in sorocarp development / actin-myosin filament sliding / adenyl nucleotide binding / hypotonic response / actomyosin contractile ring / uropod / detection of mechanical stimulus / bleb assembly / apical cortex / negative regulation of actin filament polymerization / myosin filament / myosin II complex / filopodium assembly / actomyosin / early phagosome / microfilament motor activity / cortical actin cytoskeleton organization / cortical actin cytoskeleton / pseudopodium / cleavage furrow / 14-3-3 protein binding / mitotic cytokinesis / cytoskeletal motor activity / response to cAMP / response to mechanical stimulus / cell motility / extracellular matrix / protein localization / response to hydrogen peroxide / cell cortex / chemotaxis / actin filament binding / regulation of cell shape / cytoplasmic vesicle / calmodulin binding / cytoskeleton / ATP binding / identical protein binding / cytosol
Similarity search - Function
Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Myosin tail / Myosin tail / Kinesin / Myosin N-terminal SH3-like domain ...Alpha-Beta Plaits - #1590 / Arc Repressor Mutant, subunit A - #820 / Myosin VI head, motor domain, U50 subdomain / Myosin S1 fragment, N-terminal / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #530 / Kinesin motor domain / Myosin tail / Myosin tail / Kinesin / Myosin N-terminal SH3-like domain / Myosin S1 fragment, N-terminal / 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. / IQ motif, EF-hand binding site / Kinesin motor domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / SH3 type barrels. / Arc Repressor Mutant, subunit A / Roll / Alpha-Beta Plaits / Up-down Bundle / P-loop containing nucleoside triphosphate hydrolase / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / BERYLLIUM TRIFLUORIDE ION / Myosin-2 heavy chain
Similarity search - Component
Biological speciesDictyostelium discoideum (eukaryote)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsFisher, A.J. / Holden, H.M. / Rayment, I.
Citation
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.
History
DepositionMar 21, 1995-
Revision 1.0Aug 17, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MYOSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,2674
Polymers86,7491
Non-polymers5183
Water6,756375
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.300, 182.600, 54.700
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: MOTOR DOMAIN / Mutation: Q760L, R761P, I762N
Source method: isolated from a genetically manipulated source
Details: GENETICALLY TRUNCATED HEAD OF MYOSIN FROM DICTYOSTELIUM DISCOIDEUM, LIGANDS ADP AND BEF(3)
Source: (gene. exp.) Dictyostelium discoideum (eukaryote) / Production host: Dictyostelium discoideum (eukaryote) / References: UniProt: P08799, EC: 3.6.1.32
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: 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
#4: Chemical ChemComp-BEF / BERYLLIUM TRIFLUORIDE ION


Mass: 66.007 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: BeF3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 375 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.03 Å3/Da / Density % sol: 59.41 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: batch method
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
14-5 mg/mlprotein11
28.5 %PEG800011
325 mMHEPES11
41.5 %methylpentanediol11
5170 mM11NaCl
61.8 mMADP11
71.8 mM11MgCl2
81.8 mM11BeCl2
99 mM11NaF
103 mMDTT11

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Data collection

Diffraction sourceSource: ROTATING ANODE
DetectorDate: May 1, 1994
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionRedundancy: 6.3 % / Rmerge(I) obs: 0.033
Reflection
*PLUS
Highest resolution: 2 Å / Num. obs: 63717 / % possible obs: 88 %

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Processing

Software
NameClassification
TNTrefinement
DENZOdata reduction
RefinementResolution: 2→30 Å / σ(F): 0 /
Num. reflection% reflection
obs63717 88 %
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5876 0 32 375 6283
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.015
X-RAY DIFFRACTIONt_angle_deg2.26
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_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor all: 0.191
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: t_planar_d / Dev ideal: 0.007

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