EMDB-8095: Cryo EM density of microtubule assembled from human TUBB3-D417H mutant

Basic information

• Entry: Database: EMDB / ID: EMD-8095
• Title: Cryo EM density of microtubule assembled from human TUBB3-D417H mutant
• Map data: None

Sample

• Complex: Microtubule assembled from recombinant human tubulin beta-3 D417H mutant decorated with kinesin
  • Protein or peptide: Tubulin alpha-1B chain
  • Protein or peptide: Tubulin beta-3 chain
• Ligand: GUANOSINE-5'-TRIPHOSPHATE
• Ligand: MAGNESIUM ION
• Ligand: GUANOSINE-5'-DIPHOSPHATE

• Keywords: human / microtubules / mutant tubulin / hydrolysis / STRUCTURAL PROTEIN

Function / homology

Function:

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 / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / 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

Domain/homology:

Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily

Component:

Tubulin alpha-1B chain / Tubulin beta-3 chain

• Biological species: Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 3.7 Å
• Authors: Ti SC / Pamula MC / Howes SC / Duellberg C / Cade NI / Kleiner RE / Forth S / Surrey T / Nogales E / Kapoor TM

Funding support

United States, 2 items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM65933	United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	GM051487	United States

• Citation: Journal: Dev Cell / Year: 2016; Title: Mutations in Human Tubulin Proximal to the Kinesin-Binding Site Alter Dynamic Instability at Microtubule Plus- and Minus-Ends.; Authors: Shih-Chieh Ti / Melissa C Pamula / Stuart C Howes / Christian Duellberg / Nicholas I Cade / Ralph E Kleiner / Scott Forth / Thomas Surrey / Eva Nogales / Tarun M Kapoor / ; Abstract: The assembly of microtubule-based cellular structures depends on regulated tubulin polymerization and directional transport. Here, we purify and characterize tubulin heterodimers that have human β-tubulin isotype III (TUBB3), as well as heterodimers with one of two β-tubulin mutations (D417H or R262H). Both point mutations are proximal to the kinesin-binding site and have been linked to an ocular motility disorder in humans. Compared to wild-type, microtubules with these mutations have decreased catastrophe frequencies and increased average lifetimes of plus- and minus-end-stabilizing caps. Importantly, the D417H mutation does not alter microtubule lattice structure or Mal3 binding to growing filaments. Instead, this mutation reduces the affinity of tubulin for TOG domains and colchicine, suggesting that the distribution of tubulin heterodimer conformations is changed. Together, our findings reveal how residues on the surface of microtubules, distal from the GTP-hydrolysis site and inter-subunit contacts, can alter polymerization dynamics at the plus- and minus-ends of microtubules.

History

Deposition	Mar 1, 2016	-
Header (metadata) release	Apr 20, 2016	-
Map release	Apr 20, 2016	-
Update	Mar 6, 2024	-
Current status	Mar 6, 2024	Processing site: RCSB / Status: Released