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PDBsum entry 2wbe

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protein ligands metals Protein-protein interface(s) links
Structural protein PDB id
2wbe
Jmol
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    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q2HJ86  (TBA1D_BOVIN) -  Tubulin alpha-1D chain
Seq:
Struc:
452 a.a.
412 a.a.*
Protein chain
Pfam   ArchSchema ?
Q6B856  (TBB2B_BOVIN) -  Tubulin beta-2B chain
Seq:
Struc:
445 a.a.
426 a.a.*
Protein chain
Pfam   ArchSchema ?
P46863  (KL61_DROME) -  Bipolar kinesin KRP-130
Seq:
Struc:
 
Seq:
Struc:
 
Seq:
Struc:
1066 a.a.
335 a.a.
Key:    PfamA domain  Secondary structure
* PDB and UniProt seqs differ at 11 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   6 terms 
  Biological process     microtubule-based process   5 terms 
  Biochemical function     nucleotide binding     7 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.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21326200 C.Veigel, and C.F.Schmidt (2011).
Moving into the cell: single-molecule studies of molecular motors in complex environments.
  Nat Rev Mol Cell Biol, 12, 163-176.  
21350123 J.Roostalu, C.Hentrich, P.Bieling, I.A.Telley, E.Schiebel, and T.Surrey (2011).
Directional switching of the kinesin Cin8 through motor coupling.
  Science, 332, 94-99.  
20018897 C.L.Parke, E.J.Wojcik, S.Kim, and D.K.Worthylake (2010).
ATP hydrolysis in Eg5 kinesin involves a catalytic two-water mechanism.
  J Biol Chem, 285, 5859-5867.
PDB code: 3hqd
20818331 C.Peters, K.Brejc, L.Belmont, A.J.Bodey, Y.Lee, M.Yu, J.Guo, R.Sakowicz, J.Hartman, and C.A.Moores (2010).
Insight into the molecular mechanism of the multitasking kinesin-8 motor.
  EMBO J, 29, 3437-3447.
PDB code: 3lre
20160108 C.V.Sindelar, and K.H.Downing (2010).
An atomic-level mechanism for activation of the kinesin molecular motors.
  Proc Natl Acad Sci U S A, 107, 4111-4116.  
20974813 F.J.Fourniol, C.V.Sindelar, B.Amigues, D.K.Clare, G.Thomas, M.Perderiset, F.Francis, A.Houdusse, and C.A.Moores (2010).
Template-free 13-protofilament microtubule-MAP assembly visualized at 8 A resolution.
  J Cell Biol, 191, 463-470.
PDB code: 2xrp
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.