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- PDB-1m45: CRYSTAL STRUCTURE OF MLC1P BOUND TO IQ2 OF MYO2P, A CLASS V MYOSIN -

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Basic information

Entry
Database: PDB / ID: 1m45
TitleCRYSTAL STRUCTURE OF MLC1P BOUND TO IQ2 OF MYO2P, A CLASS V MYOSIN
Components
  • IQ2 Motif from MYO2P, A Class V Myosin
  • Myosin light chain
KeywordsCELL CYCLE PROTEIN / Protein-Peptide complex / IQ motif / myosin light chain
Function / homology
Function and homology information


protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / MIH complex / RHO GTPases activate PAKs / regulation of actomyosin contractile ring contraction / peroxisome inheritance / regulation of cell wall organization or biogenesis / myosin II heavy chain binding / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle ...protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / MIH complex / RHO GTPases activate PAKs / regulation of actomyosin contractile ring contraction / peroxisome inheritance / regulation of cell wall organization or biogenesis / myosin II heavy chain binding / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / RHOT2 GTPase cycle / membrane addition at site of cytokinesis / mitochondrion inheritance / site of polarized growth / mitotic actomyosin contractile ring assembly / RHOU GTPase cycle / meiotic nuclear membrane microtubule tethering complex / cellular bud neck contractile ring / vesicle targeting / myosin V complex / vacuole inheritance / vesicle transport along actin filament / incipient cellular bud site / cellular bud tip / septum digestion after cytokinesis / Golgi inheritance / myosin V binding / cellular bud neck / mating projection tip / fungal-type vacuole membrane / vesicle docking involved in exocytosis / myosin II complex / microfilament motor activity / actin filament bundle / filamentous actin / intracellular distribution of mitochondria / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / actin filament organization / regulation of cytokinesis / small GTPase binding / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / membrane / plasma membrane / cytoplasm
Similarity search - Function
: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / 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 ...: / Class V myosin, motor domain / Dilute domain / DIL domain / Dilute domain profile. / DIL / 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 / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / P-loop containing nucleoside triphosphate hydrolase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Myosin-2 / Myosin light chain 1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT, Structure of MLC1P bound to IQ 2, 3 (SOLVED BY MAD METHOD) / Resolution: 1.65 Å
AuthorsTerrak, M. / Dominguez, R.
Citation
Journal: Embo J. / Year: 2003
Title: Two distinct myosin light chain structures are induced by specific variations within the bound IQ motifs-functional implications
Authors: Terrak, M. / Wu, G. / Stafford, W.F. / Lu, R.C. / Dominguez, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallisation, X-ray characterization and selenomethionine phasing of Mlc1p bound to IQ motifs from myosin V
Authors: Terrak, M. / Otterbein, L.R. / Wu, G. / Palecanda, L.A. / Lu, R.C. / Dominguez, R.
History
DepositionJul 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 11, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Myosin light chain
B: IQ2 Motif from MYO2P, A Class V Myosin


Theoretical massNumber of molelcules
Total (without water)19,3262
Polymers19,3262
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2630 Å2
ΔGint-18 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.594, 56.455, 56.928
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Myosin light chain / MLC1P


Mass: 16332.213 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: MLC1 / Plasmid: pAED4 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P53141
#2: Protein/peptide IQ2 Motif from MYO2P, A Class V Myosin / IQ2


Mass: 2993.420 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Saccharomyces cerevisiae (Baker's yeast).
References: UniProt: P19524
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 1.81 Å3/Da / Density % sol: 32.13 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: Si(111) double-crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.64→25.4 Å / Num. all: 17258 / Num. obs: 17258 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.3 % / Rmerge(I) obs: 0.036 / Net I/σ(I): 25.6
Reflection shellResolution: 1.64→1.71 Å / Rmerge(I) obs: 0.2 / Mean I/σ(I) obs: 6.1 / % possible all: 86

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT, Structure of MLC1P bound to IQ 2, 3 (SOLVED BY MAD METHOD)
Resolution: 1.65→25 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 2.229 / SU ML: 0.076 / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.131 / ESU R Free: 0.121 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CNS 1.0 was also used at the beginning of the refinement of this structure
RfactorNum. reflection% reflectionSelection details
Rfree0.22788 869 5.1 %RANDOM
Rwork0.19084 ---
obs0.19284 16255 98 %-
all-16255 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.235 Å2
Baniso -1Baniso -2Baniso -3
1-0.55 Å20 Å20 Å2
2--0.12 Å20 Å2
3----0.67 Å2
Refinement stepCycle: LAST / Resolution: 1.65→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1379 0 0 252 1631
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221395
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.9741882
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.0893178
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.5815273
X-RAY DIFFRACTIONr_chiral_restr0.0970.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021047
X-RAY DIFFRACTIONr_nbd_refined0.220.2751
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2185
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.266
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.150.240
X-RAY DIFFRACTIONr_mcbond_it1.0091.5869
X-RAY DIFFRACTIONr_mcangle_it1.81621405
X-RAY DIFFRACTIONr_scbond_it2.8643526
X-RAY DIFFRACTIONr_scangle_it4.7514.5477
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.275 56
Rwork0.229 1109
obs-1109

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