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- PDB-1n2d: Ternary complex of MLC1P bound to IQ2 and IQ3 of Myo2p, a class V... -

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Basic information

Entry
Database: PDB / ID: 1n2d
TitleTernary complex of MLC1P bound to IQ2 and IQ3 of Myo2p, a class V myosin
Components
  • IQ2 AND IQ3 MOTIFS FROM MYO2P, A CLASS V MYOSIN
  • Myosin Light Chain
KeywordsCELL CYCLE / 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 / mitotic actomyosin contractile ring assembly / cellular bud neck contractile ring / vesicle targeting / meiotic nuclear membrane microtubule tethering complex / site of polarized growth / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site / septum digestion after cytokinesis / cellular bud tip / myosin V binding / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / myosin II complex / vesicle transport along actin filament / fungal-type vacuole membrane / microfilament motor activity / actin filament bundle / filamentous actin / establishment of mitotic spindle orientation / transport vesicle / vesicle-mediated transport / regulation of cytokinesis / actin filament organization / actin filament binding / protein transport / actin cytoskeleton / vesicle / calmodulin binding / calcium ion binding / ATP binding / identical protein binding / plasma membrane / cytoplasm
Similarity search - Function
: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / 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. ...: / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #190 / 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 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / EF-hand domain pair / EF-hand, calcium binding motif / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair / Up-down Bundle / 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 / MAD / Resolution: 2 Å
AuthorsTerrak, M. / Wu, G. / Stafford, W.F. / Lu, R.C. / Dominguez, R.
Citation
Journal: Proc.Natl.Acad.Sci.USA / Year: 2005
Title: Structure of the light chain-binding domain of myosin V.
Authors: Terrak, M. / Rebowski, G. / Lu, R.C. / Grabarek, Z. / Dominguez, R.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2002
Title: Crystallisation, X-ray Characterixation and Selenomethionine Phasing of Mlc1p Bound to IQ motifs from Myosin V
Authors: Terrak, M. / Otterbein, L.R. / Wu, W. / Palecanda, L.A. / Lu, R.C. / Dominguez, R.
History
DepositionOct 22, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 4, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 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: Myosin Light Chain
C: IQ2 AND IQ3 MOTIFS FROM MYO2P, A CLASS V MYOSIN


Theoretical massNumber of molelcules
Total (without water)38,2083
Polymers38,2083
Non-polymers00
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-37 kcal/mol
Surface area18840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.017, 64.240, 72.785
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 / Myosin-2-Light Chain


Mass: 16332.213 Da / Num. of mol.: 2
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 AND IQ3 MOTIFS FROM MYO2P, A CLASS V MYOSIN / Myosin-2 isoform


Mass: 5543.434 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: The peptide corresponding to IQ2 and IQ3 was chemically synthesized. THE sequence of the peptide is naturally found in saccharomyces cerevisiae (baker's yeast) MYO2P, a class V myosin.
References: UniProt: P19524
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 256 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.45 Å3/Da / Density % sol: 49.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG 5000 monomethyl ether, potassium fluoride, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion
Details: Terrak, M., (2002) Acta Crystallogr.,Sect.D, 58, 1882.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mMsodium acetate1droppH4.0
21 mM1dropCaCl2
31 mMdithiothreitol1drop
410 mg/mlprotein1drop
523 %PEG5000 MME1reservoir
60.3 Mpotassium fluoride1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2001 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→41.27 Å / Num. all: 25861 / Num. obs: 25861 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 63.8 % / Biso Wilson estimate: 27.4 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17
Reflection shellResolution: 2→2.01 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 5 / % possible all: 99.1

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
Shakemodel building
SnBphasing
MLPHAREphasing
CNS1refinement
RefinementMethod to determine structure: MAD / Resolution: 2→41.27 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1510444.66 / Data cutoff high rms absF: 1510444.66 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1248 4.8 %RANDOM
Rwork0.208 ---
obs-25861 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 56.5369 Å2 / ksol: 0.36759 e/Å3
Displacement parametersBiso mean: 46.8 Å2
Baniso -1Baniso -2Baniso -3
1-5.65 Å20 Å20 Å2
2--4.98 Å20 Å2
3----10.63 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.28 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2→41.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2726 0 0 256 2982
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.65
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 198 4.8 %
Rwork0.279 3921 -
obs-3921 97.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.65

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