The mechanism of kinesin inhibition by kinesin binding protein

Abstract
Data availability
Article and author information
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Abstract

Subcellular compartmentalisation is necessary for eukaryotic cell function. Spatial and temporal regulation of kinesin activity is essential for building these local environments via control of intracellular cargo distribution. Kinesin binding protein (KBP) interacts with a subset of kinesins via their motor domains, inhibits their microtubule (MT) attachment and blocks their cellular function. However, its mechanisms of inhibition and selectivity have been unclear. Here we use cryo-electron microscopy to reveal the structure of KBP and of a KBP-kinesin motor domain complex. KBP is a TPR-containing, right-handed α-solenoid that sequesters the kinesin motor domain’s tubulin-binding surface, structurally distorting the motor domain and sterically blocking its MT attachment. KBP uses its α-solenoid concave face and edge loops to bind the kinesin motor domain, and selected structure-guided mutations disrupt KBP inhibition of kinesin transport in cells. The KBP-interacting motor domain surface contains motifs exclusively conserved in KBP-interacting kinesins, suggesting a basis for kinesin selectivity.

Data availability

Cryo-EM electron density maps and models have been deposited in the electron microscopy data bank (EMDB) and protein data bank (PDB) respectively. The relevant deposition codes are provided in Table 1.

The following data sets were generated

1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) Kinesin binding protein (KBP)
PDB, 6ZPG.

http://www.rcsb.org/structure/6ZPG
1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) Kinesin binding protein complexed with Kif15 motor domain
PDB, 6ZPH.

http://www.rcsb.org/structure/6ZPH
1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) inesin binding protein complexed with Kif15 motor domain. Symmetrised asymmetric unit.
PDB, 6ZPI.

http://www.rcsb.org/structure/6ZPI
1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) Kinesin binding protein (KBP)
EMDB, EMD- 11338.

https://www.ebi.ac.uk/pdbe/emdb/EMD- 11338
1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) Kinesin binding protein complexed with Kif15 motor domain
EMDB, EMD- 11339.

https://www.ebi.ac.uk/pdbe/emdb/EMD- 11339
1. Atherton J
2. Hummel JJA
3. Olieric N
4. Locke J
5. Peña A
6. Rosenfeld SS
7. Steinmetz MO
8. Hoogenraad CC
9. Moores CA
(2020) inesin binding protein complexed with Kif15 motor domain. Symmetrised asymmetric unit.
EMDB, EMD- 11340.

https://www.ebi.ac.uk/pdbe/emdb/EMD- 11340

Article and author information

Author details

Joseph Atherton

Randall Centre for Cell & Molecular Biophysics, King's College London, London, United Kingdom

For correspondence
joseph.atherton@kcl.ac.uk

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-6362-2347
Jessica JA Hummel

Cell Biology, Neurobiology and Biophysics, Department of Biology, Utrecht University, Utrecht, Netherlands

Competing interests
The authors declare that no competing interests exist.
Natacha Olieric

Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland

Competing interests
The authors declare that no competing interests exist.
Julia Locke

Macromolecular Machines Laboratory, The Francis Crick Institute, London, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Alejandro Peña

Department of In Silico Drug Discovery, Pharmidex 19 Pharmaceuticals, Hatfield, United Kingdom

Competing interests
The authors declare that no competing interests exist.
Steven S Rosenfeld

Department of Cancer Biology, Mayo Clinic, Jacksonville, United States

Competing interests
The authors declare that no competing interests exist.
Michel O Steinmetz

Laboratory of Biomolecular Research, Division of Biology and Chemistry, Paul Scherrer Institute, Villigen, Switzerland

Competing interests
The authors declare that no competing interests exist.
Casper C Hoogenraad

Cell Biology, Neurobiology and Biophysics, Utrecht University, Utrecht, Netherlands

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0002-2666-0758
Carolyn A Moores

Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom

Competing interests
The authors declare that no competing interests exist.

"This ORCID iD identifies the author of this article:" 0000-0001-5686-6290

Funding

Medical Research Council (MR/R000352/1)

Joseph Atherton

Worldwide Cancer Research (16-0037)

Julia Locke
Alejandro Peña

Wellcome Trust (202679/Z/16/Z,206166/Z/17/Z and 079605/Z/06/Z)

Joseph Atherton
Julia Locke
Alejandro Peña

Biotechnology and Biological Sciences Research Council (BB/L014211/1)

Joseph Atherton
Julia Locke
Alejandro Peña

National Institute of General Medical Sciences (R01GM130556)

Steven S Rosenfeld

Swiss National Science Foundation (31003A_166608)

Natacha Olieric
Michel O Steinmetz

Netherlands Organization for Scientific Research (NWO-ALW-VICI,CCH)

Jessica JA Hummel
Casper C Hoogenraad

European Research Council (ERC-consolidator,CCH)

Jessica JA Hummel
Casper C Hoogenraad

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Copyright

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.