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- PDB-1m46: CRYSTAL STRUCTURE OF MLC1P BOUND TO IQ4 OF MYO2P, A CLASS V MYOSIN -

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Basic information

Entry
Database: PDB / ID: 1m46
TitleCRYSTAL STRUCTURE OF MLC1P BOUND TO IQ4 OF MYO2P, A CLASS V MYOSIN
Components
  • IQ4 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


MIH complex / regulation of cell wall organization or biogenesis / regulation of actomyosin contractile ring contraction / RHO GTPases activate PAKs / peroxisome inheritance / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / myosin II heavy chain binding / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex ...MIH complex / regulation of cell wall organization or biogenesis / regulation of actomyosin contractile ring contraction / RHO GTPases activate PAKs / peroxisome inheritance / protein localization to cell division site involved in mitotic actomyosin contractile ring assembly / myosin II heavy chain binding / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / RHOU GTPase cycle / cellular bud neck contractile ring / vesicle targeting / meiotic nuclear membrane microtubule tethering complex / site of polarized growth / myosin V complex / mitotic actomyosin contractile ring assembly / vacuole inheritance / Golgi inheritance / incipient cellular bud site / cellular bud tip / septum digestion after cytokinesis / myosin V binding / cellular bud neck / mating projection tip / vesicle transport along actin filament / vesicle docking involved in exocytosis / fungal-type vacuole membrane / myosin II complex / microfilament motor activity / filamentous actin / actin filament bundle / establishment of mitotic spindle orientation / vesicle-mediated transport / transport vesicle / regulation of cytokinesis / actin filament organization / 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. / Myosin head, motor domain ...: / 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. / 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 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 / Molecular replacement, Based on another structure of a mutant of MLC1P bound to IQ4 that crystallized in a different space group, was determined in the lab by the se-met mad method / Resolution: 2.103 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 1.0Nov 27, 2002Provider: 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

Downloads & links

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Assembly

Deposited unit
A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin


Theoretical massNumber of molelcules
Total (without water)19,4202
Polymers19,4202
Non-polymers00
Water1,45981
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-13 kcal/mol
Surface area11210 Å2
MethodPISA
2
A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin

A: Myosin light chain
B: IQ4 Motif from MYO2P, A Class V Myosin


Theoretical massNumber of molelcules
Total (without water)38,8404
Polymers38,8404
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-x,-y+1,z1
Buried area6040 Å2
ΔGint-40 kcal/mol
Surface area20210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.504, 121.504, 29.082
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 light chain / M1c1p


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 IQ4 Motif from MYO2P, A Class V Myosin / IQ4


Mass: 3087.704 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.: 81 / 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: 2.21 Å3/Da / Density % sol: 44.25 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: ammonium sulfate, potassium/sodium tartrate, sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 4 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
12.2 Mammonium sulfate11
20.2 Mpotassium sodium tartrate tetrahydrate11
30.1 Mtrisodium citrate dihydrate11pH5.6
45 mMsodium acetate12pH4.0
51 mM12CaCl2
61 mMdithiothreitol12
710 mMprotein12

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 2000 / Details: Charles Supper Double Mirror X-ray Focusing System
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.103→45 Å / Num. all: 10540 / Num. obs: 10540 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10.4 % / Rmerge(I) obs: 0.075 / Net I/σ(I): 15
Reflection shellResolution: 2.103→2.18 Å / Rmerge(I) obs: 0.36 / Mean I/σ(I) obs: 4.2 / % possible all: 98.5
Reflection
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 45 Å / % possible obs: 99.2 %
Reflection shell
*PLUS
Highest resolution: 2.1 Å

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
REFMAC5refinement
HKL-2000data reduction
RefinementMethod to determine structure: Molecular replacement, Based on another structure of a mutant of MLC1P bound to IQ4 that crystallized in a different space group, was determined in the lab by the se-met mad method
Resolution: 2.103→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.924 / SU B: 4.782 / SU ML: 0.129 / Isotropic thermal model: overall anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.253 / ESU R Free: 0.2 / 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
Rfree0.23895 504 4.8 %RANDOM
Rwork0.19901 ---
obs0.2013 10035 99.2 %-
all-10035 --
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: 36.784 Å2
Baniso -1Baniso -2Baniso -3
1--0.56 Å20 Å20 Å2
2--0.24 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 2.103→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1388 0 0 81 1469
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221400
X-RAY DIFFRACTIONr_angle_refined_deg1.8171.9831883
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9933177
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.49615285
X-RAY DIFFRACTIONr_chiral_restr0.1410.2221
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021034
X-RAY DIFFRACTIONr_nbd_refined0.2270.2554
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1830.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2260.254
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1490.215
X-RAY DIFFRACTIONr_mcbond_it1.5421.5873
X-RAY DIFFRACTIONr_mcangle_it2.93321409
X-RAY DIFFRACTIONr_scbond_it4.4463527
X-RAY DIFFRACTIONr_scangle_it7.5744.5474
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.286 36
Rwork0.258 685
obs-685
Refinement
*PLUS
Highest resolution: 2.1 Å / Lowest resolution: 40 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.239 / Rfactor Rwork: 0.199
Solvent computation
*PLUS
Displacement parameters
*PLUS

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