PDBsum entry: 2wbe

Structural protein

PDB id: 2wbe

Contents

Protein chains

412 a.a. *

426 a.a. *

335 a.a. *

Ligands

GDP

TA1

GTP

ANP

Metals

_MG ×2

* Residue conservation analysis

PDB id:

2wbe

Name:

Structural protein

Title:

Kinesin-5-tubulin complex with amppnp

Structure:

Tubulin alpha-1d chain. Chain: a. Synonym: alpha-beta-tubulin, tuba1d. Tubulin beta-2b chain. Chain: b. Synonym: alpha-beta-tubulin, tubb2b. Bipolar kinesin krp-130. Chain: c. Fragment: motor domain with neck linker, residues 1-368.

Source:

Bos taurus. Cattle. Organism_taxid: 9913. Organ: brain. Drosophila melanogaster. Common fruit fly. Organism_taxid: 7227. Expressed in: escherichia coli. Expression_system_taxid: 469008.

Authors:

A.J.Bodey,M.Kikkawa,C.A.Moores

Key ref:

A.J.Bodey et al. (2009). 9-Angström structure of a microtubule-bound mitotic motor. J Mol Biol, 388, 218-224. PubMed id: 19285086 DOI: 10.1016/j.jmb.2009.03.008

Date:

26-Feb-09 Release date: 24-Mar-09

Protein chain

P02550  (TBA1A_PIG) -  Tubulin alpha-1A chain

Seq: 451 a.a.

Struc: 412 a.a.*

Protein chain

P02554  (TBB_PIG) -  Tubulin beta chain

Seq: 445 a.a.

Struc: 426 a.a.

Protein chain

P46863  (KL61_DROME) -  Bipolar kinesin KRP-130

Seq: 1066 a.a.

Struc: 335 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: protein complex (2 terms)
• Biological process: microtubule-based process (4 terms)
• Biochemical function: structural molecule activity (6 terms)

DOI no: 10.1016/j.jmb.2009.03.008

J Mol Biol 388:218-224 (2009)

PubMed id: 19285086

9-Angström structure of a microtubule-bound mitotic motor.

A.J.Bodey, M.Kikkawa, C.A.Moores.

ABSTRACT

Kinesin-5 (K5) motors are important components of the microtubule (MT)-based cell division machinery and are targets for small-molecule inhibitors currently in cancer clinical trials. However, the nature of the K5-MT interaction and the regulatory mechanisms that control it remain unclear. Using cryo-electron microscopy and image processing, we calculated the structure of a K5 motor bound to MTs at 9 A resolution, providing insight into this important interaction. Our reconstruction reveals the K5 motor domain in an ATP-like conformation in which MT binding induces the conserved nucleotide-sensing switch I and II loops to form a compact subdomain around the bound nucleotide. Our reconstruction also reveals a novel conformation for the K5-specific drug-binding loop 5, suggesting a possible role for it in switching K5s between force generation and diffusional modes of MT binding. Our data thus shed light on regulation of the interaction between spindle components important for chromosome segregation.

Selected figure(s)

Figure 2.
Fig. 2. ATP conformation of K5-MD bound to MTs. (a) Homology models of K5-MD prepared against “ATP-like” (purple) and “ADP-like” (green) templates. The MT-binding surface faces the viewer with the α4 relay helix running roughly horizontally. α4 is shown in red in the “ATP-like” conformation. The nucleotide-binding pocket is at the N-terminus of α4 (on the right in this view) with the nucleotide shown in a ball-and-stick representation. T-Coffee^31 was used for multiple sequence alignment and Modeller (9v1) was used to generate homology models.^32 A number of representative kinesin MD crystal structures were used to generate KLP61F-MD homology models—namely, 1MKJ, 1T5C and 2KIN for the “ATP-like” state and 1II6, 1F9T, 2GRY and 1I5S for the “ADP-like” state—based on multivariate statistical analysis.^30 UCSF Chimera^33 was used for visualisation and rigid-body docking. Fits were first performed manually and were then refined computationally. (b) Fitting of the K5 homology models into the EM density for (i) “ATP-like” (purple) and (ii) “ADP-like” (green) conformations. The reconstruction is shown as white transparency at 0.5 σ unless otherwise stated. The well-conserved MT-binding regions of ATP-K5-MD (β5a, loop 12, α6) are highlighted in yellow. (c) Slab through the reconstruction viewed from the MT plus-end with both “ATP-like” (purple, red α4) and “ADP-like” (green) models shown. The reconstruction is also shown at 1.5 σ in grey mesh, clearly identifying the tube of density corresponding to α4 at the MT interface. (d) The well-defined nucleotide-binding subdomain formed by switch I and II loops (outlined in yellow) beneath α3 is induced by MT binding. These loops are only partly represented in the homology models due to disorder in the templates. The grey mesh (1.5 σ) shows the well-defined nature of the nucleotide-binding subdomain. (e) Location of density (dotted black outline) occupied by the N- and C-terminal residues of the K5 construct, close to each other in our reconstruction, demonstrating that the K5 neck-linker is docked in its ATP MT-bound conformation. N- and C-terminal residues are highlighted and labelled in yellow.

Figure 3.
Fig. 3. Loop 5 adopts a flattened conformation against α3. Fitting of the K5-ADP-based homology model^43 (green) and the K5-ADP-drug-based homology model^44 (brown). The two adjacent K5 motors give different views of the same fits. Loop 5 from both models protrudes from the reconstruction but could be accommodated by unoccupied EM density nearby (dotted outline). α3 of both homology models protrudes from the EM density adjacent to the nucleotide-binding subdomain.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2009, 388, 218-224) copyright 2009.

Figures were selected by the author.