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Yorodumi- PDB-1n2d: Ternary complex of MLC1P bound to IQ2 and IQ3 of Myo2p, a class V... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1n2d | ||||||
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Title | Ternary complex of MLC1P bound to IQ2 and IQ3 of Myo2p, a class V myosin | ||||||
Components |
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Keywords | CELL 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 / 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 | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å | ||||||
Authors | Terrak, 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1n2d.cif.gz | 84.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1n2d.ent.gz | 64.6 KB | Display | PDB format |
PDBx/mmJSON format | 1n2d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1n2d_validation.pdf.gz | 375.9 KB | Display | wwPDB validaton report |
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Full document | 1n2d_full_validation.pdf.gz | 380.1 KB | Display | |
Data in XML | 1n2d_validation.xml.gz | 8.1 KB | Display | |
Data in CIF | 1n2d_validation.cif.gz | 13.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/n2/1n2d ftp://data.pdbj.org/pub/pdb/validation_reports/n2/1n2d | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | 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 | | 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 / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 2 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.75 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 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 diffusionDetails: Terrak, M., (2002) Acta Crystallogr.,Sect.D, 58, 1882. | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Aug 1, 2001 / Details: Bent conical Si-mirror (Rh coating) |
Radiation | Monochromator: Bent Ge(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2→2.01 Å / Rmerge(I) obs: 0.423 / Mean I/σ(I) obs: 5 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method 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
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 56.5369 Å2 / ksol: 0.36759 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.8 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2→41.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.13 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
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Xplor file |
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Refinement | *PLUS % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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