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- PDB-2xrp: Human Doublecortin N-DC Repeat (1MJD) and Mammalian Tubulin (1JFF... -
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Open data
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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 | |||||||||
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![]() | STRUCTURAL PROTEIN | |||||||||
Function / homology | ![]() axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / 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 ...axoneme assembly / Neurofascin interactions / positive regulation of axon guidance / microtubule associated complex / microtubule organizing center / 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 / nervous system development / mitotic cell cycle / microtubule binding / microtubule / cytoskeleton / hydrolase activity / intracellular signal transduction / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / protein kinase binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 8.2 Å | |||||||||
![]() | Fourniol, F.J. / Sindelar, C.V. / Amigues, B. / Clare, D.K. / Thomas, G. / Perderiset, M. / Francis, F. / Houdusse, A. / Moores, C.A. | |||||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 682.7 KB | Display | ![]() |
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PDB format | ![]() | 545.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 1.4 MB | Display | ![]() |
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Full document | ![]() | 1.8 MB | Display | |
Data in XML | ![]() | 157.7 KB | Display | |
Data in CIF | ![]() | 221.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1788MC ![]() 1787C M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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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) ![]() ![]() #2: Protein | Mass: 50236.352 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() #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.) ![]() ![]() ![]() #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 |
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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 |
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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: ![]() |
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 |
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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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