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Yorodumi- PDB-6qve: NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qve | |||||||||||||||||||||
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Title | NgCKK (Naegleria Gruberi CKK) decorated 14pf taxol-GDP microtubule | |||||||||||||||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Microtubule CAMSAP Calmodulin-regulated spectrum-associated proteins CKK Cryo-EM Cryo-Electron Microscopy | |||||||||||||||||||||
Function / homology | Function and homology information microtubule minus-end / microtubule minus-end binding / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of microtubule depolymerization / Intraflagellar transport ...microtubule minus-end / microtubule minus-end binding / odontoblast differentiation / Post-chaperonin tubulin folding pathway / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / negative regulation of microtubule depolymerization / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / COPI-independent Golgi-to-ER retrograde traffic / Kinesins / Hedgehog 'off' state / Assembly and cell surface presentation of NMDA receptors / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / intercellular bridge / regulation of synapse organization / nuclear envelope lumen / MHC class I protein binding / cytoplasmic microtubule / Recycling pathway of L1 / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / spindle assembly / cellular response to interleukin-4 / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Resolution of Sister Chromatid Cohesion / MHC class II antigen presentation / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / PKR-mediated signaling / mitotic spindle / structural constituent of cytoskeleton / microtubule cytoskeleton organization / HCMV Early Events / Aggrephagy / cytoplasmic ribonucleoprotein granule / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / azurophil granule lumen / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-stranded RNA binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / mitotic cell cycle / cell body / microtubule / Potential therapeutics for SARS / cytoskeleton / calmodulin binding / membrane raft / protein domain specific binding / cell division / GTPase activity / ubiquitin protein ligase binding / Neutrophil degranulation / GTP binding / protein-containing complex binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytosol / cytoplasm Similarity search - Function | |||||||||||||||||||||
Biological species | Naegleria gruberi (eukaryote) Homo sapiens (human) | |||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å | |||||||||||||||||||||
Authors | Atherton, J.M. / Luo, Y. / Xiang, S. / Yang, C. / Jiang, K. / Stangier, M. / Vemu, A. / Cook, A. / Wang, S. / Roll-Mecak, A. ...Atherton, J.M. / Luo, Y. / Xiang, S. / Yang, C. / Jiang, K. / Stangier, M. / Vemu, A. / Cook, A. / Wang, S. / Roll-Mecak, A. / Steinmetz, M.O. / Akhmanova, A. / Baldus, M. / Moores, C.A. | |||||||||||||||||||||
Funding support | United Kingdom, Netherlands, Switzerland, 6items
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Citation | Journal: Nat Commun / Year: 2019 Title: Structural determinants of microtubule minus end preference in CAMSAP CKK domains. Authors: Joseph Atherton / Yanzhang Luo / Shengqi Xiang / Chao Yang / Ankit Rai / Kai Jiang / Marcel Stangier / Annapurna Vemu / Alexander D Cook / Su Wang / Antonina Roll-Mecak / Michel O Steinmetz ...Authors: Joseph Atherton / Yanzhang Luo / Shengqi Xiang / Chao Yang / Ankit Rai / Kai Jiang / Marcel Stangier / Annapurna Vemu / Alexander D Cook / Su Wang / Antonina Roll-Mecak / Michel O Steinmetz / Anna Akhmanova / Marc Baldus / Carolyn A Moores / Abstract: CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To ...CAMSAP/Patronins regulate microtubule minus-end dynamics. Their end specificity is mediated by their CKK domains, which we proposed recognise specific tubulin conformations found at minus ends. To critically test this idea, we compared the human CAMSAP1 CKK domain (HsCKK) with a CKK domain from Naegleria gruberi (NgCKK), which lacks minus-end specificity. Here we report near-atomic cryo-electron microscopy structures of HsCKK- and NgCKK-microtubule complexes, which show that these CKK domains share the same protein fold, bind at the intradimer interprotofilament tubulin junction, but exhibit different footprints on microtubules. NMR experiments show that both HsCKK and NgCKK are remarkably rigid. However, whereas NgCKK binding does not alter the microtubule architecture, HsCKK remodels its microtubule interaction site and changes the underlying polymer structure because the tubulin lattice conformation is not optimal for its binding. Thus, in contrast to many MAPs, the HsCKK domain can differentiate subtly specific tubulin conformations to enable microtubule minus-end recognition. | |||||||||||||||||||||
History |
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-Structure visualization
Movie |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6qve.cif.gz | 331.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qve.ent.gz | 267 KB | Display | PDB format |
PDBx/mmJSON format | 6qve.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qve_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 6qve_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 6qve_validation.xml.gz | 51.7 KB | Display | |
Data in CIF | 6qve_validation.cif.gz | 77.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qv/6qve ftp://data.pdbj.org/pub/pdb/validation_reports/qv/6qve | HTTPS FTP |
-Related structure data
Related structure data | 4650MC 4643C 4644C 4654C 6qusC 6quyC 6qvjC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein , 3 types, 5 molecules CAWHG
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GTP / Source: (natural) Homo sapiens (human) / Cell line: tsa201 cells / Tissue: Embryonic Kidney / References: UniProt: P68363 #2: Protein | | Mass: 20879.051 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Naegleria gruberi (eukaryote) / Gene: NAEGRDRAFT_50049 / Production host: Escherichia coli (E. coli) / References: UniProt: D2VJG4 #3: Protein | Mass: 49717.629 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: GDP Taxol / Source: (natural) Homo sapiens (human) / Cell line: tsa201 / Tissue: embryonic kidney / References: UniProt: A0A2K5HGL3, UniProt: P07437*PLUS |
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-Non-polymers , 4 types, 8 molecules
#4: Chemical | #5: Chemical | #6: Chemical | #7: 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
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Source (natural) |
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Source (recombinant) | Organism: Escherichia coli (E. coli) | ||||||||||||||||||||||||
Buffer solution | pH: 6.8 / Details: BRB20 | ||||||||||||||||||||||||
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: 42 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Details: dose weighted images used in final reconstructions |
-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: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 28421 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL | ||||||||||||||||||||||||
Refine LS restraints |
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