+Open data
-Basic information
Entry | Database: PDB / ID: 3edl | ||||||
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Title | Kinesin13-Microtubule Ring complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Kinesin / Kinesin13 / Kin-I / M-Kinesin / Microtubule / Tubulin / depolymerization | ||||||
Function / homology | Function and homology information postsynaptic cytoskeleton organization / regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / metaphase chromosome alignment / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic ...postsynaptic cytoskeleton organization / regulation of chromosome segregation / establishment or maintenance of microtubule cytoskeleton polarity / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / metaphase chromosome alignment / Kinesins / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases Activate Formins / Separation of Sister Chromatids / microtubule plus-end / attachment of mitotic spindle microtubules to kinetochore / MHC class II antigen presentation / microtubule plus-end binding / microtubule depolymerization / regulation of neurotransmitter receptor localization to postsynaptic specialization membrane / microtubule motor activity / kinesin complex / mitotic metaphase chromosome alignment / microtubule-based movement / chromosome, centromeric region / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / kinetochore / microtubule cytoskeleton organization / spindle / presynapse / mitotic cell cycle / microtubule binding / postsynapse / microtubule / hydrolase activity / cell division / GTPase activity / centrosome / glutamatergic synapse / GTP binding / ATP hydrolysis activity / ATP binding / nucleus / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Bos taurus (cattle) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 28 Å | ||||||
Authors | Tan, D. / Rice, W.J. / Sosa, H. | ||||||
Citation | Journal: Structure / Year: 2008 Title: Structure of the kinesin13-microtubule ring complex. Authors: Dongyan Tan / William J Rice / Hernando Sosa / Abstract: To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron ...To investigate the mechanism of kinesin13-induced microtubule depolymerization, we have calculated a three-dimensional (3D) map of the kinesin13-microtubule ring complex, using cryo-electron microscopy (cryo-EM) and image analysis. An atomic model of the complex was produced by docking the crystal structures of tubulin and a kinesin13 motor domain (MD) into the 3D map. The model reveals a snapshot of the depolymerization mechanism by providing a 3D view of the complex formed between the kinesin13 MD and a curved tubulin protofilament (pf). It suggests that contacts mediated by kinesin13 class-specific residues in the putative microtubule-binding site stabilize intra-dimer tubulin curvature. In addition, a tubulin-binding site on the kinesin13 MD was identified. Mutations at this class-conserved site selectively disrupt the formation of microtubule-associated ring complexes. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 3edl.cif.gz | 393.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3edl.ent.gz | 304.7 KB | Display | PDB format |
PDBx/mmJSON format | 3edl.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3edl_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 3edl_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 3edl_validation.xml.gz | 77 KB | Display | |
Data in CIF | 3edl_validation.cif.gz | 113 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ed/3edl ftp://data.pdbj.org/pub/pdb/validation_reports/ed/3edl | HTTPS FTP |
-Related structure data
Related structure data | 5027MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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3 |
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Symmetry | Helical symmetry: (Circular symmetry: 1 / Dyad axis: no / N subunits divisor: 1 / Num. of operations: 33 / Rise per n subunits: 5.506 Å / Rotation per n subunits: 168.1 °) |
-Components
-Tubulin alpha-1A ... , 2 types, 2 molecules AF
#1: Protein | Mass: 50107.238 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02550 |
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#4: Protein | Mass: 50163.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02550 |
-Protein , 2 types, 3 molecules BGD
#2: Protein | Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Tissue: brain / References: UniProt: P02554 #3: Protein | | Mass: 37072.609 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: DmKlp10A / Plasmid: pRSET B / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q922S8 |
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-Non-polymers , 8 types, 118 molecules
#5: Chemical | ChemComp-ZN / | ||||||||||||
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#6: Chemical | #7: Chemical | #8: Chemical | #9: Chemical | ChemComp-TA1 / | #10: Chemical | ChemComp-ANP / | #11: Chemical | ChemComp-CN2 / | #12: Water | ChemComp-HOH / | |
-Details
Sequence details | DBREF IS NOT PROVIDED BECAUSE THE STRUCTURES USED TO GENERATE THE MODELS WERE DERIVED FROM ...DBREF IS NOT PROVIDED BECAUSE THE STRUCTURES |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: Kinesin13-Microtubule ring complex / Type: COMPLEX |
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Buffer solution | pH: 6.8 Details: 80 mM Pipes, pH 6.8, 2 mM MgCl2, 1 mM EGTA, 2 mM AMP-PNP, 0.02 mM taxol |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: 400 mesh Quantifoil grid R2/4 |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 50000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 1500 nm |
Image recording | Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: Each particle | ||||||||||||||||||||||||
3D reconstruction | Method: HELICAL / Resolution: 28 Å / Nominal pixel size: 2.5 Å / Details: Helical Fourier-Bessel / Symmetry type: HELICAL | ||||||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST
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