+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4644 | |||||||||
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Title | NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule | |||||||||
Map data | NgCKK-13pf microtubule symmetrised reconstruction (1x asymmetric unit, local resolution filtered) | |||||||||
Sample |
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Keywords | Microtubule CAMSAP Calmodulin-regulated spectrum-associated proteins CKK Cryo-EM Cryo-Electron Microscopy / STRUCTURAL PROTEIN | |||||||||
Function / homology | Function and homology information microtubule minus-end / odontoblast differentiation / Post-chaperonin tubulin folding pathway / microtubule minus-end binding / 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 / Intraflagellar transport / cytoskeleton-dependent intracellular transport ...microtubule minus-end / odontoblast differentiation / Post-chaperonin tubulin folding pathway / microtubule minus-end binding / 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 / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC / Gap junction assembly / negative regulation of microtubule depolymerization / COPI-independent Golgi-to-ER retrograde traffic / natural killer cell mediated cytotoxicity / Assembly and cell surface presentation of NMDA receptors / Kinesins / GTPase activating protein binding / COPI-dependent Golgi-to-ER retrograde traffic / 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 / spindle assembly / RHO GTPases activate IQGAPs / cellular response to interleukin-4 / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / cytoplasmic microtubule organization / 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 / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / AURKA Activation by TPX2 / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / PKR-mediated signaling / structural constituent of cytoskeleton / mitotic spindle / Aggrephagy / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / azurophil granule lumen / double-stranded RNA binding / 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 / protein-containing complex binding / GTP binding / structural molecule activity / protein-containing complex / extracellular exosome / extracellular region / nucleus / metal ion binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Naegleria gruberi (eukaryote) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Atherton JM / Luo Y | |||||||||
Funding support | United Kingdom, Switzerland, 2 items
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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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_4644.map.gz | 642.1 KB | EMDB map data format | |
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Header (meta data) | emd-4644-v30.xml emd-4644.xml | 17.7 KB 17.7 KB | Display Display | EMDB header |
Images | emd_4644.png | 180.1 KB | ||
Filedesc metadata | emd-4644.cif.gz | 6.9 KB | ||
Others | emd_4644_additional.map.gz | 167.8 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4644 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4644 | HTTPS FTP |
-Validation report
Summary document | emd_4644_validation.pdf.gz | 223.9 KB | Display | EMDB validaton report |
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Full document | emd_4644_full_validation.pdf.gz | 223 KB | Display | |
Data in XML | emd_4644_validation.xml.gz | 4.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4644 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-4644 | HTTPS FTP |
-Related structure data
Related structure data | 6quyMC 4643C 4650C 4654C 6qusC 6qveC 6qvjC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_4644.map.gz / Format: CCP4 / Size: 307.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | NgCKK-13pf microtubule symmetrised reconstruction (1x asymmetric unit, local resolution filtered) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: NgCKK-13pf microtubule C1 reconstruction (full map, local resolution...
File | emd_4644_additional.map | ||||||||||||
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Annotation | NgCKK-13pf microtubule C1 reconstruction (full map, local resolution filtered) | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule
+Supramolecule #1: NgCKK (N.Gruberi CKK) decorated 13pf taxol-GDP microtubule
+Supramolecule #2: tubulin
+Supramolecule #3: N.Gruberi CKK
+Macromolecule #1: Tubulin alpha-1B chain
+Macromolecule #2: CKK domain protein
+Macromolecule #3: Tubulin beta chain
+Macromolecule #4: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #5: MAGNESIUM ION
+Macromolecule #6: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #7: TAXOL
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 6.8 / Details: BRB20 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 42.0 e/Å2 / Details: dose weighted images used in final reconstructions |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 27635 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: OTHER |
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Output model | PDB-6quy: |