+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-41022 | |||||||||
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Title | Map of Tubulin Tyrosine Ligase Like 6 | |||||||||
Map data | Map of TTLL6 bound to unmodified human microtubules, obtained by focused classification and refinement | |||||||||
Sample |
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Keywords | Tubulin polyglutamylase / tubulin post-translational modifications / microtubules / TTLL / LIGASE | |||||||||
Function / homology | Function and homology information positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation ...positive regulation of cilium movement / protein-glutamic acid ligase activity / tubulin-glutamic acid ligase activity / Carboxyterminal post-translational modifications of tubulin / protein polyglutamylation / regulation of cilium beat frequency involved in ciliary motility / 9+0 non-motile cilium / microtubule severing / Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) / microtubule bundle formation / tubulin binding / ciliary basal body / cilium / microtubule cytoskeleton organization / microtubule / ATP binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 7.2 Å | |||||||||
Authors | Mahalingan KK / Grotjahn D / Li Y / Lander GC / Zehr EA / Roll-Mecak A | |||||||||
Funding support | United States, 1 items
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Citation | Journal: Nat Chem Biol / Year: 2024 Title: Structural basis for α-tubulin-specific and modification state-dependent glutamylation. Authors: Kishore K Mahalingan / Danielle A Grotjahn / Yan Li / Gabriel C Lander / Elena A Zehr / Antonina Roll-Mecak / Abstract: Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. ...Microtubules have spatiotemporally complex posttranslational modification patterns. Tubulin tyrosine ligase-like (TTLL) enzymes introduce the most prevalent modifications on α-tubulin and β-tubulin. How TTLLs specialize for specific substrate recognition and ultimately modification-pattern generation is largely unknown. TTLL6, a glutamylase implicated in ciliopathies, preferentially modifies tubulin α-tails in microtubules. Cryo-electron microscopy, kinetic analysis and single-molecule biochemistry reveal an unprecedented quadrivalent recognition that ensures simultaneous readout of microtubule geometry and posttranslational modification status. By binding to a β-tubulin subunit, TTLL6 modifies the α-tail of the longitudinally adjacent tubulin dimer. Spanning two tubulin dimers along and across protofilaments (PFs) ensures fidelity of recognition of both the α-tail and the microtubule. Moreover, TTLL6 reads out and is stimulated by glutamylation of the β-tail of the laterally adjacent tubulin dimer, mediating crosstalk between α-tail and β-tail. This positive feedback loop can generate localized microtubule glutamylation patterns. Our work uncovers general principles that generate tubulin chemical and topographic complexity. | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_41022.map.gz | 4.4 MB | EMDB map data format | |
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Header (meta data) | emd-41022-v30.xml emd-41022.xml | 20.1 KB 20.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_41022_fsc.xml emd_41022_fsc_2.xml | 20.2 KB 20 KB | Display Display | FSC data file |
Images | emd_41022.png | 44.6 KB | ||
Masks | emd_41022_msk_1.map | 699 MB | Mask map | |
Filedesc metadata | emd-41022.cif.gz | 6.3 KB | ||
Others | emd_41022_half_map_1.map.gz emd_41022_half_map_2.map.gz | 557.9 MB 557.5 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-41022 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-41022 | HTTPS FTP |
-Related structure data
Related structure data | 8t42C 8u3zC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_41022.map.gz / Format: CCP4 / Size: 699 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Map of TTLL6 bound to unmodified human microtubules, obtained by focused classification and refinement | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.15 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_41022_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: First half-map of TTLL6 bound to unmodified human...
File | emd_41022_half_map_1.map | ||||||||||||
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Annotation | First half-map of TTLL6 bound to unmodified human microtubules, obtained by focused classification and refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Second half-map of TTLL6 bound to unmodified human...
File | emd_41022_half_map_2.map | ||||||||||||
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Annotation | Second half-map of TTLL6 bound to unmodified human microtubules, obtained by focused classification and refinement | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : TTLL6 bound to unmodified human microtubules
Entire | Name: TTLL6 bound to unmodified human microtubules |
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Components |
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-Supramolecule #1: TTLL6 bound to unmodified human microtubules
Supramolecule | Name: TTLL6 bound to unmodified human microtubules / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all Details: Microtubules were decorated with TTLL6 on electron microscopy grids |
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Source (natural) | Organism: Mus musculus (house mouse) / Location in cell: cytoplasm |
Molecular weight | Theoretical: 20 KDa |
-Macromolecule #1: Tubulin Tyrosine Ligase Like 6
Macromolecule | Name: Tubulin Tyrosine Ligase Like 6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO / EC number: ec: 6.3.2.61 |
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Source (natural) | Organism: Mus musculus (house mouse) |
Recombinant expression | Organism: Escherichia coli 0.1304 (bacteria) |
Sequence | String: GKKKRKKKRL VINLSNCRYD SVRRAAQQYG LREAGDNDDW TLYWTDYSVS LERVMEMKSY QKINHFPGMS EICRKDLLAR NMSRMLKLFP KDFHFFPRTW CLPADWGDLQ TYSRTRKNKT YICKPDSGCQ GRGIFITRSV KEIKPGEDMI CQLYISKPFI IDGFKFDLRV ...String: GKKKRKKKRL VINLSNCRYD SVRRAAQQYG LREAGDNDDW TLYWTDYSVS LERVMEMKSY QKINHFPGMS EICRKDLLAR NMSRMLKLFP KDFHFFPRTW CLPADWGDLQ TYSRTRKNKT YICKPDSGCQ GRGIFITRSV KEIKPGEDMI CQLYISKPFI IDGFKFDLRV YVLVTSCDPL RVFVYNEGLA RFATTSYSHP NLDNLDEICM HLTNYSINKH SSNFVQDAFS GSKRKLSTFN SYMKTHGYDV EQIWRGIEDV IIKTLISAHP VIKHNYHTCF PSHTLNSACF EILGFDILLD RKLKPWLLEV NHSPSFSTDS KLDKEVKDSL LYDALVLINL GNCDKKKVLE EERQRGRFLQ QCPNREIRLE EVKGFQAMRL QKTEEYEKKN CGGFRLIYPG LNLEKYDKFF QDNSSLFQNT VASRARELYA RQLIQELRQK QEKKVFLKKA RKA UniProtKB: Tubulin polyglutamylase TTLL6 |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL | ||||||||||||||||||
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Buffer | pH: 7 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR | ||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 303 K / Instrument: FEI VITROBOT MARK IV Details: The sample was blotted with Whatman #5 blotting paper on both sides of the grid for 3 s with a blot offset of -1 using a Vitrobot Mark IV (Thermo Fisher Scientific) with a chamber set to 30C ...Details: The sample was blotted with Whatman #5 blotting paper on both sides of the grid for 3 s with a blot offset of -1 using a Vitrobot Mark IV (Thermo Fisher Scientific) with a chamber set to 30C at 100% humidity and subsequently plunged into liquid ethane.. | ||||||||||||||||||
Details | TTLL6 decoration of microtubule was heterogenous |
-Electron microscopy
Microscope | FEI TALOS ARCTICA |
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Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 36000 |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-39 / Number real images: 2771 / Average exposure time: 9.75 sec. / Average electron dose: 42.0 e/Å2 |
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |