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Yorodumi- PDB-5m50: Mechanism of microtubule minus-end recognition and protection by ... -
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-Basic information
Entry | Database: PDB / ID: 5m50 | |||||||||||||||||||||
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Title | Mechanism of microtubule minus-end recognition and protection by CAMSAP proteins | |||||||||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / CAMSAP CKK Microtubule Tubulin | |||||||||||||||||||||
Function / homology | Function and homology information regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / protein transport along microtubule / microtubule anchoring / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III ...regulation of organelle organization / zonula adherens maintenance / microtubule minus-end / protein transport along microtubule / microtubule anchoring / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / RHO GTPases activate IQGAPs / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / microtubule minus-end binding / RHO GTPases Activate Formins / regulation of Golgi organization / establishment or maintenance of microtubule cytoskeleton polarity / MHC class II antigen presentation / cilium movement / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / epithelial cell-cell adhesion / The role of GTSE1 in G2/M progression after G2 checkpoint / zonula adherens / Separation of Sister Chromatids / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Recruitment of NuMA to mitotic centrosomes / Regulation of PLK1 Activity at G2/M Transition / Hedgehog 'off' state / negative regulation of microtubule depolymerization / establishment of epithelial cell apical/basal polarity / motile cilium / positive regulation of axon guidance / embryo development ending in birth or egg hatching / regulation of focal adhesion assembly / spectrin binding / regulation of microtubule polymerization / axoneme / microtubule-based process / regulation of microtubule cytoskeleton organization / cytoplasmic microtubule organization / regulation of cell migration / ciliary basal body / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / structural constituent of cytoskeleton / microtubule cytoskeleton organization / actin filament binding / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / in utero embryonic development / microtubule / calmodulin binding / hydrolase activity / protein heterodimerization activity / GTPase activity / centrosome / GTP binding / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||||||||||||||
Biological species | Mus musculus (house mouse) Bos taurus (cattle) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.3 Å | |||||||||||||||||||||
Authors | Akhmanova, A. / Moores, C.A. / Baldus, M. / Steinmetz, M.O. / Topf, M. / Roberts, A.J. / Grant, B.J. / Scarabelli, G. / Joseph, A.-P. / van Hooff, J.J.E. ...Akhmanova, A. / Moores, C.A. / Baldus, M. / Steinmetz, M.O. / Topf, M. / Roberts, A.J. / Grant, B.J. / Scarabelli, G. / Joseph, A.-P. / van Hooff, J.J.E. / Houben, K. / Hua, S. / Luo, Y. / Stangier, M.M. / Jiang, K. / Atherton, J. | |||||||||||||||||||||
Funding support | United Kingdom, United States, Netherlands, Switzerland, 6items
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Citation | Journal: Nat Struct Mol Biol / Year: 2017 Title: A structural model for microtubule minus-end recognition and protection by CAMSAP proteins. Authors: Joseph Atherton / Kai Jiang / Marcel M Stangier / Yanzhang Luo / Shasha Hua / Klaartje Houben / Jolien J E van Hooff / Agnel-Praveen Joseph / Guido Scarabelli / Barry J Grant / Anthony J ...Authors: Joseph Atherton / Kai Jiang / Marcel M Stangier / Yanzhang Luo / Shasha Hua / Klaartje Houben / Jolien J E van Hooff / Agnel-Praveen Joseph / Guido Scarabelli / Barry J Grant / Anthony J Roberts / Maya Topf / Michel O Steinmetz / Marc Baldus / Carolyn A Moores / Anna Akhmanova / Abstract: CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization ...CAMSAP and Patronin family members regulate microtubule minus-end stability and localization and thus organize noncentrosomal microtubule networks, which are essential for cell division, polarization and differentiation. Here, we found that the CAMSAP C-terminal CKK domain is widely present among eukaryotes and autonomously recognizes microtubule minus ends. Through a combination of structural approaches, we uncovered how mammalian CKK binds between two tubulin dimers at the interprotofilament interface on the outer microtubule surface. In vitro reconstitution assays combined with high-resolution fluorescence microscopy and cryo-electron tomography suggested that CKK preferentially associates with the transition zone between curved protofilaments and the regular microtubule lattice. We propose that minus-end-specific features of the interprotofilament interface at this site serve as the basis for CKK's minus-end preference. The steric clash between microtubule-bound CKK and kinesin motors explains how CKK protects microtubule minus ends against kinesin-13-induced depolymerization and thus controls the stability of free microtubule minus ends. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5m50.cif.gz | 335.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5m50.ent.gz | 267.6 KB | Display | PDB format |
PDBx/mmJSON format | 5m50.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5m50_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 5m50_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 5m50_validation.xml.gz | 53.4 KB | Display | |
Data in CIF | 5m50_validation.cif.gz | 79 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m5/5m50 ftp://data.pdbj.org/pub/pdb/validation_reports/m5/5m50 | HTTPS FTP |
-Related structure data
Related structure data | 4154MC 3444C 4156C 5lznC 5m54C 5m5cC 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
-Protein , 3 types, 5 molecules DAEBC
#1: Protein | Mass: 48769.988 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: F2Z4C1, UniProt: P81947*PLUS #2: Protein | Mass: 47940.945 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / References: UniProt: Q6B856 #3: Protein | | Mass: 13431.391 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Camsap3, Kiaa1543 / Production host: Escherichia coli (E. coli) / References: UniProt: Q80VC9 |
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-Non-polymers , 5 types, 16 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | #8: Water | ChemComp-HOH / | |
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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
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 6.8 / Details: BRB80 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: 13pf Microtubules | ||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid type: C-flat-2/2 | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK III / 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: INTEGRATING / Film or detector model: DIRECT ELECTRON DE-20 (5k x 3k) / Details: 25e-/A2 used in final reconstuctions |
-Processing
Software | Name: PHENIX / Version: 1.11.1_2575: / Classification: refinement | ||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 5.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 6530 Details: Gold-standard noise substitution test used to asses for over fitting (Chen et al., 2013) Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER | ||||||||||||||||||||||||
Refine LS restraints |
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