+Open data
-Basic information
Entry | Database: PDB / ID: 2kin | ||||||
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Title | KINESIN (MONOMERIC) FROM RATTUS NORVEGICUS | ||||||
Components | (KINESIN) x 2 | ||||||
Keywords | MOTOR PROTEIN / CYTOSKELETON | ||||||
Function / homology | Function and homology information response to rotenone / RHO GTPases activate KTN1 / Kinesins / distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / COPI-dependent Golgi-to-ER retrograde traffic / anterograde dendritic transport of neurotransmitter receptor complex / central region of growth cone / anterograde axonal protein transport / MHC class II antigen presentation ...response to rotenone / RHO GTPases activate KTN1 / Kinesins / distal axon / anterograde dendritic transport of messenger ribonucleoprotein complex / COPI-dependent Golgi-to-ER retrograde traffic / anterograde dendritic transport of neurotransmitter receptor complex / central region of growth cone / anterograde axonal protein transport / MHC class II antigen presentation / retrograde neuronal dense core vesicle transport / apolipoprotein receptor binding / thalamus development / intracellular mRNA localization / apical dendrite / cellular response to ethanol / motor neuron axon guidance / plus-end-directed microtubule motor activity / microtubule motor activity / ciliary rootlet / kinesin complex / synaptic vesicle transport / postsynaptic cytosol / kinesin binding / microtubule-based process / GABA-ergic synapse / mRNA transport / neuron development / axonal growth cone / vesicle-mediated transport / axon cytoplasm / dendrite cytoplasm / cellular response to nerve growth factor stimulus / axon guidance / hippocampus development / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / P-body / cerebral cortex development / scaffold protein binding / microtubule binding / perikaryon / microtubule / neuron projection / axon / neuronal cell body / dendrite / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / ATP binding / cytoplasm Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Sack, S. / Muller, J. / Kozielski, F. / Marx, A. / Thormahlen, M. / Biou, V. / Mandelkow, E.-M. / Brady, S.T. / Mandelkow, E. | ||||||
Citation | Journal: Biochemistry / Year: 1997 Title: X-ray structure of motor and neck domains from rat brain kinesin. Authors: Sack, S. / Muller, J. / Marx, A. / Thormahlen, M. / Mandelkow, E.M. / Brady, S.T. / Mandelkow, E. #1: Journal: J.Struct.Biol. / Year: 1997 Title: Crystallization and Preliminary X-Ray Analysis of the Single-Headed and Double-Headed Motor Protein Kinesin Authors: Kozielski, F. / Schonbrunn, E. / Sack, S. / Muller, J. / Brady, S.T. / Mandelkow, E. #2: Journal: Cell(Cambridge,Mass.) / Year: 1997 Title: The Crystal Structure of Dimeric Kinesin and Implications for Microtubule-Dependent Motility Authors: Kozielski, F. / Sack, S. / Marx, A. / Thormahlen, M. / Schonbrunn, E. / Biou, V. / Thompson, A. / Mandelkow, E.M. / Mandelkow, E. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2kin.cif.gz | 85.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2kin.ent.gz | 63.7 KB | Display | PDB format |
PDBx/mmJSON format | 2kin.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2kin_validation.pdf.gz | 469.4 KB | Display | wwPDB validaton report |
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Full document | 2kin_full_validation.pdf.gz | 480 KB | Display | |
Data in XML | 2kin_validation.xml.gz | 10.2 KB | Display | |
Data in CIF | 2kin_validation.cif.gz | 15.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ki/2kin ftp://data.pdbj.org/pub/pdb/validation_reports/ki/2kin | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27072.869 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, MOTOR DOMAIN / Mutation: G293D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: P56536*PLUS | ||||
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#2: Protein | Mass: 11169.800 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, MOTOR DOMAIN / Mutation: G293D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Organ: BRAIN / Production host: Escherichia coli (E. coli) / References: UniProt: Q6QLM7*PLUS | ||||
#3: Chemical | #4: Chemical | ChemComp-ADP / | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.46 Å3/Da / Density % sol: 49.6 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 7.5 Details: HANGING DROP METHOD WAS USED. PROTEIN WAS CRYSTALLIZED FROM 20MM PIPES, PH 7.5, 50MM KCL, 1MM EGTA, 1MM DTT, 0.9 M LI2SO4. THE RESERVOIR CONTAINED 1.8 M LITHIUM SULFATE IN THE SAME BUFFER., ...Details: HANGING DROP METHOD WAS USED. PROTEIN WAS CRYSTALLIZED FROM 20MM PIPES, PH 7.5, 50MM KCL, 1MM EGTA, 1MM DTT, 0.9 M LI2SO4. THE RESERVOIR CONTAINED 1.8 M LITHIUM SULFATE IN THE SAME BUFFER., vapor diffusion - hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 28, 1996 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. obs: 32107 / % possible obs: 99.3 % / Redundancy: 5.1 % / Rsym value: 0.048 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 4.2 % / Rsym value: 0.19 / % possible all: 98.8 |
Reflection | *PLUS Num. measured all: 301422 / Rmerge(I) obs: 0.048 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: UNREFINED KINESIN DIMER Resolution: 2→6 Å / Cross valid method: FREE R
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Refinement step | Cycle: LAST / Resolution: 2→6 Å
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.194 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS Biso mean: 24.3 Å2 | ||||||||||||||||||||
Refine LS restraints | *PLUS
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