+Open data
-Basic information
Entry | Database: PDB / ID: 6e7b | |||||||||
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Title | 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubules | |||||||||
Components |
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Keywords | STRUCTURAL PROTEIN / cytoskeleton / microtubules / recombinant human tubulin / tubulin isotype | |||||||||
Function / homology | Function and homology information netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Sealing of the nuclear envelope (NE) by ESCRT-III / Intraflagellar transport / cytoskeleton-dependent intracellular transport / Formation of tubulin folding intermediates by CCT/TriC ...netrin receptor binding / Post-chaperonin tubulin folding pathway / dorsal root ganglion development / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / 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 / COPI-independent Golgi-to-ER retrograde traffic / Prefoldin mediated transfer of substrate to CCT/TriC / Assembly and cell surface presentation of NMDA receptors / Kinesins / COPI-dependent Golgi-to-ER retrograde traffic / intercellular bridge / Recycling pathway of L1 / cytoplasmic microtubule / microtubule-based process / RHOH GTPase cycle / RHO GTPases activate IQGAPs / cellular response to interleukin-4 / Hedgehog 'off' state / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / filopodium / cell periphery / Translocation of SLC2A4 (GLUT4) to the plasma membrane / RHO GTPases Activate Formins / peptide binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / axon guidance / PKR-mediated signaling / structural constituent of cytoskeleton / mitotic spindle / Aggrephagy / microtubule cytoskeleton organization / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / double-stranded RNA binding / lamellipodium / mitotic cell cycle / growth cone / microtubule / cell division / axon / GTPase activity / neuronal cell body / ubiquitin protein ligase binding / dendrite / GTP binding / structural molecule activity / extracellular exosome / nucleus / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Ti, S.C. / Alushin, G.M. / Kapoor, T.M. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Dev Cell / Year: 2018 Title: Human β-Tubulin Isotypes Can Regulate Microtubule Protofilament Number and Stability. Authors: Shih-Chieh Ti / Gregory M Alushin / Tarun M Kapoor / Abstract: Cell biological studies have shown that protofilament number, a fundamental feature of microtubules, can correlate with the expression of different tubulin isotypes. However, it is not known if ...Cell biological studies have shown that protofilament number, a fundamental feature of microtubules, can correlate with the expression of different tubulin isotypes. However, it is not known if tubulin isotypes directly control this basic microtubule property. Here, we report high-resolution cryo-EM reconstructions (3.5-3.65 Å) of purified human α1B/β3 and α1B/β2B microtubules and find that the β-tubulin isotype can determine protofilament number. Comparisons of atomic models of 13- and 14-protofilament microtubules reveal how tubulin subunit plasticity, manifested in "accordion-like" distributed structural changes, can accommodate distinct lattice organizations. Furthermore, compared to α1B/β3 microtubules, α1B/β2B filaments are more stable to passive disassembly and against depolymerization by MCAK or chTOG, microtubule-associated proteins with distinct mechanisms of action. Mixing tubulin isotypes in different proportions results in microtubules with protofilament numbers and stabilities intermediate to those of isotypically pure filaments. Together, our findings indicate that microtubule protofilament number and stability can be controlled through β-tubulin isotype composition. | |||||||||
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 | 6e7b.cif.gz | 161.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6e7b.ent.gz | 125 KB | Display | PDB format |
PDBx/mmJSON format | 6e7b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6e7b_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 6e7b_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6e7b_validation.xml.gz | 41.1 KB | Display | |
Data in CIF | 6e7b_validation.cif.gz | 57.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e7/6e7b ftp://data.pdbj.org/pub/pdb/validation_reports/e7/6e7b | HTTPS FTP |
-Related structure data
Related structure data | 8997MC 8998C 6e7cC 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
#1: Protein | Mass: 47809.926 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBB3, TUBB4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q13509 | ||||
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#2: Protein | Mass: 48665.027 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TUBA1B / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P68363 | ||||
#3: Chemical | #4: Chemical | ChemComp-G2P / | #5: Chemical | ChemComp-GTP / | |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: HELICAL ARRAY / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: 13-pf 3-start GMPCPP-human alpha1B/beta3 microtubule decorated with kinesin-1 motor domain Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Source (recombinant) | Organism: Trichoplusia ni (cabbage looper) |
Buffer solution | pH: 6.8 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: pseudo-helical microtubule |
Specimen support | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Cs: 2.7 mm / C2 aperture diameter: 100 µm |
Image recording | Average exposure time: 0.2 sec. / Electron dose: 1.6 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Movie frames/image: 50 / Used frames/image: 2-50 |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: -27.66 ° / Axial rise/subunit: 9.474 Å / Axial symmetry: C1 | ||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 68858 / Symmetry type: HELICAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: RECIPROCAL | ||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 3JAT Accession code: 3JAT / Source name: PDB / Type: experimental model |