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Open data
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Basic information
Entry | Database: PDB / ID: 5lt2 | ||||||||||||
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Title | nucleotide-free kinesin-1 motor domain, P1 crystal form | ||||||||||||
![]() | Kinesin-like protein | ||||||||||||
![]() | MOTOR PROTEIN / Kinesin motor domain / ADP dissociation / nucleotide-free | ||||||||||||
Function / homology | ![]() cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization ...cytoplasm organization / cytolytic granule membrane / plus-end-directed vesicle transport along microtubule / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / anterograde neuronal dense core vesicle transport / anterograde axonal protein transport / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / lysosome localization / positive regulation of potassium ion transport / natural killer cell mediated cytotoxicity / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate KTN1 / stress granule disassembly / mitochondrion transport along microtubule / ciliary rootlet / centrosome localization / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / synaptic vesicle transport / Insulin processing / microtubule-based movement / centriolar satellite / axon cytoplasm / MHC class II antigen presentation / dendrite cytoplasm / phagocytic vesicle / regulation of membrane potential / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / axon guidance / cellular response to type II interferon / Signaling by ALK fusions and activated point mutants / mitotic cell cycle / microtubule binding / microtubule / vesicle / cadherin binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | ![]() | ||||||||||||
Method | ![]() ![]() ![]() | ||||||||||||
![]() | Cao, L. / Gigant, B. | ||||||||||||
Funding support | ![]()
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![]() | ![]() Title: The structural switch of nucleotide-free kinesin. Authors: Cao, L. / Cantos-Fernandes, S. / Gigant, B. | ||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 707.2 KB | Display | ![]() |
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PDB format | ![]() | 585.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 492.6 KB | Display | ![]() |
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Full document | ![]() | 515.2 KB | Display | |
Data in XML | ![]() | 67.3 KB | Display | |
Data in CIF | ![]() | 93.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5lt0C ![]() 5lt1C ![]() 5lt3C ![]() 5lt4C ![]() 4lnuS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 36276.746 Da / Num. of mol.: 6 / Mutation: C7S, C65A, C168A, C174S, C294A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | ChemComp-SO4 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.71 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 50 mM Mes pH 6.5 0.16 M ammonium sulfate 30% mPEG 5000 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→49 Å / Num. obs: 59440 / % possible obs: 98 % / Redundancy: 3.5 % / CC1/2: 0.985 / Rrim(I) all: 0.23 / Net I/σ(I): 6.8 |
Reflection shell | Rrim(I) all: 1.61 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LNU Resolution: 2.6→38.401 Å / SU ML: 0.37 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 28.6
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→38.401 Å
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Refine LS restraints |
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LS refinement shell |
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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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