[English] 日本語
Yorodumi- PDB-4atx: Rigor kinesin motor domain with an ordered neck-linker, docked on... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4atx | ||||||
---|---|---|---|---|---|---|---|
Title | Rigor kinesin motor domain with an ordered neck-linker, docked on tubulin dimer, modelled into the 8A cryo-EM map of doublecortin- microtubules decorated with kinesin | ||||||
Components |
| ||||||
Keywords | HYDROLASE / MICROTUBULE / NECK-LINKER | ||||||
Function / homology | Function and homology information regulation of modification of synapse structure, modulating synaptic transmission / RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / membrane-bounded organelle / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex ...regulation of modification of synapse structure, modulating synaptic transmission / RHO GTPases activate KTN1 / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / membrane-bounded organelle / plus-end-directed vesicle transport along microtubule / cytoplasm organization / cytolytic granule membrane / mitocytosis / anterograde dendritic transport of neurotransmitter receptor complex / positive regulation of vesicle fusion / anterograde axonal protein transport / MHC class II antigen presentation / retrograde neuronal dense core vesicle transport / vesicle transport along microtubule / positive regulation of intracellular protein transport / lysosome localization / positive regulation of potassium ion transport / JUN kinase binding / plus-end-directed microtubule motor activity / stress granule disassembly / positive regulation of axon guidance / mitochondrion transport along microtubule / centrosome localization / ciliary rootlet / microtubule motor activity / natural killer cell mediated cytotoxicity / kinesin complex / microtubule lateral binding / postsynaptic cytosol / synaptic vesicle transport / positive regulation of insulin secretion involved in cellular response to glucose stimulus / endocytic vesicle / microtubule-based process / axonal growth cone / phagocytic vesicle / axon cytoplasm / dendrite cytoplasm / regulation of membrane potential / axon guidance / hippocampus development / positive regulation of synaptic transmission, GABAergic / positive regulation of protein localization to plasma membrane / cellular response to type II interferon / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / nervous system development / microtubule binding / vesicle / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein-containing complex binding / perinuclear region of cytoplasm / ATP hydrolysis activity / mitochondrion / ATP binding / identical protein binding / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | RATTUS NORVEGICUS (Norway rat) BOS TAURUS (cattle) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 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. #1: Journal: J Cell Biol / Year: 2010 Title: Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution. Authors: Franck J Fourniol / Charles V Sindelar / Béatrice Amigues / Daniel K Clare / Geraint Thomas / Mylène Perderiset / Fiona Francis / Anne Houdusse / Carolyn A Moores / Abstract: Microtubule-associated proteins (MAPs) are essential for regulating and organizing cellular microtubules (MTs). However, our mechanistic understanding of MAP function is limited by a lack of detailed ...Microtubule-associated proteins (MAPs) are essential for regulating and organizing cellular microtubules (MTs). However, our mechanistic understanding of MAP function is limited by a lack of detailed structural information. Using cryo-electron microscopy and single particle algorithms, we solved the 8 Å structure of doublecortin (DCX)-stabilized MTs. Because of DCX's unusual ability to specifically nucleate and stabilize 13-protofilament MTs, our reconstruction provides unprecedented insight into the structure of MTs with an in vivo architecture, and in the absence of a stabilizing drug. DCX specifically recognizes the corner of four tubulin dimers, a binding mode ideally suited to stabilizing both lateral and longitudinal lattice contacts. A striking consequence of this is that DCX does not bind the MT seam. DCX binding on the MT surface indirectly stabilizes conserved tubulin-tubulin lateral contacts in the MT lumen, operating independently of the nucleotide bound to tubulin. DCX's exquisite binding selectivity uncovers important insights into regulation of cellular MTs. | ||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 4atx.cif.gz | 234 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4atx.ent.gz | 182 KB | Display | PDB format |
PDBx/mmJSON format | 4atx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4atx_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4atx_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 4atx_validation.xml.gz | 54.6 KB | Display | |
Data in CIF | 4atx_validation.cif.gz | 77.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/4atx ftp://data.pdbj.org/pub/pdb/validation_reports/at/4atx | HTTPS FTP |
-Related structure data
Related structure data | 2098MC 2095C 4atuC C: citing same article (ref.) M: map data used to model this data |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
#1: Protein | Mass: 49907.770 Da / Num. of mol.: 1 / 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.: 1 / 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: 38136.984 Da / Num. of mol.: 1 / Fragment: MOTOR DOMAIN, RESIDUES 1-340 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q2PQA9, EC: 3.6.4.4 |
#4: Chemical | ChemComp-GDP / |
#5: Chemical | ChemComp-GTP / |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: DOUBLECORTIN-STABILISED MICROTUBULES DECORATED WITH KINESIN MOTOR DOMAINS Type: COMPLEX |
---|---|
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 |
---|---|
Microscopy | Model: FEI TECNAI F20 / Date: Sep 1, 2009 |
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: 2900 nm / Nominal defocus min: 760 nm / Cs: 2 mm |
Specimen holder | Temperature: 93 K |
Image recording | Electron dose: 15 e/Å2 / Film or detector model: KODAK SO-163 FILM |
Image scans | Num. digital images: 63 |
Radiation wavelength | Relative weight: 1 |
-Processing
EM software |
| |||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Details: DONE WITH FREALIGN | |||||||||||||||||||||
3D reconstruction | Method: SINGLE PARTICLE / Resolution: 8.2 Å / Num. of particles: 168000 / Nominal pixel size: 2.8 Å Details: A HOMOLOGY MODEL OF RAT KINESIN MOTOR DOMAIN MUTANT T93N WAS GENERATED USING MODELLER, BASED ON THE STRUCTURE OF HUMAN KINESIN 1BG2. 2) KINESIN LOOP11 (AA 237-254) WAS OMITTED IN THIS MODEL ...Details: A HOMOLOGY MODEL OF RAT KINESIN MOTOR DOMAIN MUTANT T93N WAS GENERATED USING MODELLER, BASED ON THE STRUCTURE OF HUMAN KINESIN 1BG2. 2) KINESIN LOOP11 (AA 237-254) WAS OMITTED IN THIS MODEL AS NO CRYSTAL STRUCTURE REFLECTED THE CONFORMATION OF LOOP11 VISUALISED IN THE EM MAP SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2098. (DEPOSITION ID: 10790). Symmetry type: HELICAL | |||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL / Target criteria: Cross-correlation coefficient / Details: METHOD--RIGID BODY | |||||||||||||||||||||
Atomic model building |
| |||||||||||||||||||||
Refinement | Highest resolution: 8.2 Å | |||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.2 Å
|