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Yorodumi- PDB-2xrp: Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2xrp | |||||||||
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Title | Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF and 3HKE) Docked into the 8-Angstrom Cryo-EM Map of Doublecortin- Stabilised Microtubules | |||||||||
Components |
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Keywords | STRUCTURAL 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: 8.2 Å | |||||||||
Authors | Fourniol, F.J. / Sindelar, C.V. / Amigues, B. / Clare, D.K. / Thomas, G. / Perderiset, M. / Francis, F. / Houdusse, A. / Moores, C.A. | |||||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 2xrp.cif.gz | 682.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2xrp.ent.gz | 545.1 KB | Display | PDB format |
PDBx/mmJSON format | 2xrp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2xrp_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2xrp_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 2xrp_validation.xml.gz | 157.7 KB | Display | |
Data in CIF | 2xrp_validation.cif.gz | 221.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xr/2xrp ftp://data.pdbj.org/pub/pdb/validation_reports/xr/2xrp | HTTPS FTP |
-Related structure data
Related structure data | 1788MC 1787C 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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1 |
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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: 11029.393 Da / Num. of mol.: 1 / Fragment: RESIDUES 46-140 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Organ: BRAIN / Plasmid: PFASTBAC / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / Strain (production host): SF9 / References: UniProt: O43602 #4: Chemical | ChemComp-GDP / #5: Chemical | ChemComp-GTP / Sequence details | CHIMERIC SEQUENCE OF SHEEP AND CATTLE MAIN ALPHA-TUBULIN ISOFORMS (1JFF AND 3HKE) | |
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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: MICROTUBULES NUCLEATED AND STABILISED BY DOUBLECORTIN / Type: COMPLEX |
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Buffer solution | Name: 80MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP / pH: 6.8 Details: 80MM PIPES, 1MM EGTA, 3MM MGCL2, 1MM TCEP, 0.5MM GTP |
Specimen | Conc.: 1.2 mg/ml / 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: LIQUID 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: 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 |
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CTF correction | Details: DONE IN FREALIGN | ||||||||||||||||||||||||||||
3D reconstruction | Method: CUSTOM SCRIPTS, PROJECTION MATCHING / Resolution: 8.2 Å / Num. of particles: 168000 / Nominal pixel size: 2.8 Å Details: THE STRUCTURE WAS DETERMINED IN THE ABSENCE OF A STABILISING DRUG. SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-1788. (DEPOSITION ID: 7535). Symmetry type: HELICAL | ||||||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Target criteria: Cross-correlation coefficient Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--ELECTRON CRYSTALLOGRAPHY | ||||||||||||||||||||||||||||
Atomic model building |
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Refinement | Highest resolution: 8.2 Å | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 8.2 Å
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