+Open data
-Basic information
Entry | Database: PDB / ID: 6ixr | ||||||||||||
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Title | Structure of Myo2-GTD in complex with Inp2 | ||||||||||||
Components |
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Keywords | PROTEIN BINDING / Cargo binding domain | ||||||||||||
Function / homology | Function and homology information : / peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance ...: / peroxisome inheritance / RHOT2 GTPase cycle / RHOT1 GTPase cycle / Myo2p-Vac17p-Vac8p transport complex / membrane addition at site of cytokinesis / meiotic nuclear membrane microtubule tethering complex / myosin V complex / vacuole inheritance / Golgi inheritance / incipient cellular bud site / cellular bud tip / vesicle docking involved in exocytosis / cellular bud neck / mating projection tip / vesicle transport along actin filament / fungal-type vacuole membrane / microfilament motor activity / actin filament bundle / filamentous actin / establishment of mitotic spindle orientation / protein-membrane adaptor activity / transport vesicle / vesicle-mediated transport / actin filament organization / actin filament binding / actin cytoskeleton / protein transport / vesicle / calmodulin binding / ATP binding / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.854 Å | ||||||||||||
Authors | Tang, K. / Wei, Z. | ||||||||||||
Funding support | China, 3items
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Citation | Journal: J.Biol.Chem. / Year: 2019 Title: Structural mechanism for versatile cargo recognition by the yeast class V myosin Myo2. Authors: Tang, K. / Li, Y. / Yu, C. / Wei, Z. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ixr.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ixr.ent.gz | 141 KB | Display | PDB format |
PDBx/mmJSON format | 6ixr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ix/6ixr ftp://data.pdbj.org/pub/pdb/validation_reports/ix/6ixr | HTTPS FTP |
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-Related structure data
Related structure data | 6ixoC 6ixpC 6ixqC 2f6hS S: Starting model for refinement C: citing same article (ref.) |
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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: 48900.484 Da / Num. of mol.: 1 / Mutation: Deletions 1342-1347 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: MYO2, CDC66, YOR326W, O6167 / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P19524 |
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#2: Protein/peptide | Mass: 2623.817 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast) Strain: ATCC 204508 / S288c / Gene: INP2, YMR163C, YM8520.12C / Plasmid: modified pET32a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q03824 |
#3: Chemical |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.41 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 8% w/v PEG 4000, 0.2-0.3 M lithium/ammonium sulfate pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 30, 2018 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.85→55 Å / Num. obs: 13042 / % possible obs: 99.9 % / Redundancy: 19 % / Biso Wilson estimate: 79.08 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.172 / Rpim(I) all: 0.041 / Rrim(I) all: 0.177 / Net I/σ(I): 14.5 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F6H Resolution: 2.854→49.446 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.49
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.14 Å2 / Biso mean: 93.3167 Å2 / Biso min: 50.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.854→49.446 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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