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Yorodumi- PDB-4atu: Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) do... -
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-Basic information
Entry | Database: PDB / ID: 4atu | ||||||
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Title | Human doublecortin N-DC repeat plus linker, and tubulin (2XRP) docked into an 8A cryo-EM map of doublecortin-stabilised microtubules reconstructed in absence of kinesin | ||||||
Components |
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Keywords | HYDROLASE / MICROTUBULE-ASSOCIATED PROTEIN | ||||||
Function / homology | Function and homology information axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule-based process / central nervous system development / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / neuron migration / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / retina development in camera-type eye / mitotic cell cycle / nervous system development / microtubule binding / microtubule / cytoskeleton / intracellular signal transduction / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) BOS TAURUS (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.3 Å | ||||||
Authors | Liu, J.S. / Schubert, C.R. / Fu, X. / Fourniol, F.J. / Jaiswal, J.K. / Houdusse, A. / Stultz, C.M. / Moores, C.A. / Walsh, C.A. | ||||||
Citation | Journal: Mol Cell / Year: 2012 Title: Molecular basis for specific regulation of neuronal kinesin-3 motors by doublecortin family proteins. Authors: Judy S Liu / Christian R Schubert / Xiaoqin Fu / Franck J Fourniol / Jyoti K Jaiswal / Anne Houdusse / Collin M Stultz / Carolyn A Moores / Christopher A Walsh / Abstract: Doublecortin (Dcx) defines a growing family of microtubule (MT)-associated proteins (MAPs) involved in neuronal migration and process outgrowth. We show that Dcx is essential for the function of ...Doublecortin (Dcx) defines a growing family of microtubule (MT)-associated proteins (MAPs) involved in neuronal migration and process outgrowth. We show that Dcx is essential for the function of Kif1a, a kinesin-3 motor protein that traffics synaptic vesicles. Neurons lacking Dcx and/or its structurally conserved paralogue, doublecortin-like kinase 1 (Dclk1), show impaired Kif1a-mediated transport of Vamp2, a cargo of Kif1a, with decreased run length. Human disease-associated mutations in Dcx's linker sequence (e.g., W146C, K174E) alter Kif1a/Vamp2 transport by disrupting Dcx/Kif1a interactions without affecting Dcx MT binding. Dcx specifically enhances binding of the ADP-bound Kif1a motor domain to MTs. Cryo-electron microscopy and subnanometer-resolution image reconstruction reveal the kinesin-dependent conformational variability of MT-bound Dcx and suggest a model for MAP-motor crosstalk on MTs. Alteration of kinesin run length by MAPs represents a previously undiscovered mode of control of kinesin transport and provides a mechanism for regulation of MT-based transport by local signals. | ||||||
History |
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-Structure visualization
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
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PDBx/mmCIF format | 4atu.cif.gz | 678.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4atu.ent.gz | 542.4 KB | Display | PDB format |
PDBx/mmJSON format | 4atu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4atu_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 4atu_full_validation.pdf.gz | 1.9 MB | Display | |
Data in XML | 4atu_validation.xml.gz | 163 KB | Display | |
Data in CIF | 4atu_validation.cif.gz | 226.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4atu ftp://data.pdbj.org/pub/pdb/validation_reports/at/4atu | HTTPS FTP |
-Related structure data
Related structure data | 2095MC 2098C 4atxC 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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-Components
#1: Protein | Mass: 49907.770 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q6B856, EC: 3.6.5.6 #2: Protein | Mass: 50236.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) BOS TAURUS (cattle) / Organ: BRAIN / References: UniProt: Q2HJ86, EC: 3.6.5.6 #3: Protein | | Mass: 41604.727 Da / Num. of mol.: 1 / Fragment: RESIDUES 2-360 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: O43602 #4: Chemical | ChemComp-GDP / #5: Chemical | ChemComp-GTP / Sequence details | FULL-LENGTH HUMAN DOUBLECORT | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DOUBLECORTIN-STABILISED MICROTUBULES / Type: COMPLEX |
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Buffer solution | Name: 20MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP / pH: 6.8 Details: 20MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE Details: CRYOGEN- ETHANE, HUMIDITY- 100, INSTRUMENT- FEI VITROBOT |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai F20 / Image courtesy: FEI Company |
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Microscopy | Model: FEI TECNAI F20 / Date: Oct 1, 2010 |
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: 3600 nm / Nominal defocus min: 900 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K |
Image recording | Electron dose: 17 e/Å2 / Film or detector model: KODAK SO-163 FILM |
-Processing
EM software |
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CTF correction | Details: DONE WITH FREALIGN | |||||||||||||||
3D reconstruction | Method: SINGLE PARTICLE / Resolution: 8.3 Å / Num. of particles: 146000 / Nominal pixel size: 2.8 Å Details: DOUBLECORTIN LINKER REGION 151-156 WAS MODELLED INTO THE EM MAP USING CHIMERA AND REFINED USING FLEX-EM SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2095. (DEPOSITION ID: 10785). Symmetry type: HELICAL | |||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY | |||||||||||||||
Atomic model building | PDB-ID: 2XRP Accession code: 2XRP / Source name: PDB / Type: experimental model | |||||||||||||||
Refinement | Highest resolution: 8.3 Å | |||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.3 Å
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