EMDB-10422: Human kinesin-5 motor domain in the AMPPNP state bound to microtubules

Basic information

• Entry: Database: EMDB / ID: EMD-10422
• Title: Human kinesin-5 motor domain in the AMPPNP state bound to microtubules

Sample

• Complex: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
  • Complex: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
    • Protein or peptide: Tubulin beta chain
    • Protein or peptide: Tubulin alpha-1B chain
  • Complex: AMPPNP bound Human Eg5 motor domain in complex with alpha/beta tubulin
    • Protein or peptide: Kinesin-like protein KIF11
• Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER
• Ligand: MAGNESIUM ION
• Ligand: GUANOSINE-5'-TRIPHOSPHATE
• Ligand: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

• Keywords: kinesin / microtubule / mitosis / inhibition / motor / CELL CYCLE

Function / homology

Function:

spindle elongation / regulation of mitotic centrosome separation / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / Kinesins / plus-end-directed microtubule motor activity / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / mitotic centrosome separation / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / COPI-dependent Golgi-to-ER retrograde traffic / microtubule motor activity / kinesin complex / spindle organization / microtubule-based movement / mitotic spindle assembly / MHC class II antigen presentation / mitotic spindle organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / spindle microtubule / structural constituent of cytoskeleton / mitotic spindle / spindle pole / microtubule cytoskeleton organization / spindle / microtubule cytoskeleton / mitotic cell cycle / microtubule binding / microtubule / cell division / GTPase activity / GTP binding / protein kinase binding / protein-containing complex / ATP binding / membrane / nucleus / metal ion binding / cytoplasm / cytosol

Domain/homology:

Kinesin-associated microtubule-binding domain / Kinesin-associated microtubule-binding / : / : / Kinesin motor domain signature. / Kinesin motor domain, conserved site / Kinesin motor domain / Kinesin motor domain profile. / Kinesin motor, catalytic domain. ATPase. / Kinesin motor domain / Kinesin motor domain superfamily / 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 / P-loop containing nucleoside triphosphate hydrolase

Component:

Tubulin beta chain / Kinesin-like protein KIF11 / Tubulin alpha-1B chain

• Biological species: Sus scrofa (pig) / Homo sapiens (human)
• Method: helical reconstruction / cryo EM / Resolution: 6.1 Å
• Authors: Pena AP / Sweeney A

Funding support

United Kingdom, 4 items

Organization	Grant number	Country
Wellcome Trust	202679/Z/16/Z and 206166/Z/17/Z	United Kingdom
Medical Research Council (United Kingdom)	MR/J003867/1	United Kingdom
Medical Research Council (United Kingdom)	MR/N013867/1	United Kingdom
Worldwide Cancer Research

• Citation: Journal: Structure / Year: 2020; Title: Structure of Microtubule-Trapped Human Kinesin-5 and Its Mechanism of Inhibition Revealed Using Cryoelectron Microscopy.; Authors: Alejandro Peña / Aaron Sweeney / Alexander D Cook / Julia Locke / Maya Topf / Carolyn A Moores / ; Abstract: Kinesin-5 motors are vital mitotic spindle components, and disruption of their function perturbs cell division. We investigated the molecular mechanism of the human kinesin-5 inhibitor GSK-1, which allosterically promotes tight microtubule binding. GSK-1 inhibits monomeric human kinesin-5 ATPase and microtubule gliding activities, and promotes the motor's microtubule stabilization activity. Using cryoelectron microscopy, we determined the 3D structure of the microtubule-bound motor-GSK-1 at 3.8 Å overall resolution. The structure reveals that GSK-1 stabilizes the microtubule binding surface of the motor in an ATP-like conformation, while destabilizing regions of the motor around the empty nucleotide binding pocket. Density corresponding to GSK-1 is located between helix-α4 and helix-α6 in the motor domain at its interface with the microtubule. Using a combination of difference mapping and protein-ligand docking, we characterized the kinesin-5-GSK-1 interaction and further validated this binding site using mutagenesis. This work opens up new avenues of investigation of kinesin inhibition and spindle perturbation.

History

Deposition	Oct 29, 2019	-
Header (metadata) release	Dec 18, 2019	-
Map release	Mar 4, 2020	-
Update	May 22, 2024	-
Current status	May 22, 2024	Processing site: PDBe / Status: Released