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Yorodumi- PDB-6rev: Cryo-EM structure of the N-terminal DC repeat (NDC) of human doub... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6rev | ||||||
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Title | Cryo-EM structure of the N-terminal DC repeat (NDC) of human doublecortin (DCX) bound to 13-protofilament GDP-microtubule | ||||||
Components |
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Keywords | CYTOSOLIC PROTEIN / Microtubule-associated protein / neuronal migration protein / ubiquitin-like fold | ||||||
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 / 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: 3.8 Å | ||||||
Authors | Manka, S.W. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: EMBO Rep / Year: 2020 Title: Pseudo-repeats in doublecortin make distinct mechanistic contributions to microtubule regulation. Authors: Szymon W Manka / Carolyn A Moores / Abstract: Doublecortin (DCX) is a neuronal microtubule-associated protein (MAP) indispensable for brain development. Its flexibly linked doublecortin (DC) domains-NDC and CDC-mediate microtubule (MT) ...Doublecortin (DCX) is a neuronal microtubule-associated protein (MAP) indispensable for brain development. Its flexibly linked doublecortin (DC) domains-NDC and CDC-mediate microtubule (MT) nucleation and stabilization, but it is unclear how. Using high-resolution time-resolved cryo-EM, we mapped NDC and CDC interactions with tubulin at different MT polymerization stages and studied their functional effects on MT dynamics using TIRF microscopy. Although coupled, each DC repeat within DCX appears to have a distinct role in MT nucleation and stabilization: CDC is a conformationally plastic module that appears to facilitate MT nucleation and stabilize tubulin-tubulin contacts in the nascent MT lattice, while NDC appears to be favored along the mature lattice, providing MT stabilization. Our structures of MT-bound DC domains also explain in unprecedented detail the DCX mutation-related brain defects observed in the clinic. This modular composition of DCX reflects a common design principle among MAPs where pseudo-repeats of tubulin/MT binding elements chaperone or stabilize distinct conformational transitions to regulate distinct stages of MT dynamic instability. | ||||||
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 | 6rev.cif.gz | 325.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rev.ent.gz | 260.7 KB | Display | PDB format |
PDBx/mmJSON format | 6rev.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6rev_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6rev_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6rev_validation.xml.gz | 46.3 KB | Display | |
Data in CIF | 6rev_validation.cif.gz | 71.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/re/6rev ftp://data.pdbj.org/pub/pdb/validation_reports/re/6rev | HTTPS FTP |
-Related structure data
Related structure data | 4858MC 4861C 4863C 6rf2C 6rfdC 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
-Protein , 3 types, 5 molecules NbBAa
#1: Protein | Mass: 11441.834 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCX, DBCN, LISX / Production host: Escherichia coli (E. coli) / References: UniProt: O43602 | ||
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#2: Protein | Mass: 48113.129 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | Mass: 48263.594 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: P81947 |
-Non-polymers , 3 types, 6 molecules
#4: Chemical | #5: Chemical | #6: Chemical | |
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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 |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 6.8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 25 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Width: 5 / Height: 5 |
-Processing
EM software | Name: PHENIX / Category: model fitting |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30434 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: Cross-correlation coefficient |
Atomic model building | PDB-ID: 1MJD Accession code: 1MJD / Source name: PDB / Type: experimental model |