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protein ligands metals Protein-protein interface(s) links
Transport protein PDB id
2p4n
Jmol
Contents
Protein chains
323 a.a. *
412 a.a. *
426 a.a. *
Ligands
ADP
GTP
GDP
TA1
Metals
_MG ×2
_ZN
* Residue conservation analysis
PDB id:
2p4n
Name: Transport protein
Title: Human monomeric kinesin (1bg2) and bovine tubulin (1jff) docked into the 9-angstrom cryo-em map of nucleotide-free kinesin complexed to the microtubule
Structure: Kinesin heavy chain. Chain: k. Fragment: k349 construct of human kinesin. Synonym: ubiquitous kinesin heavy chain, ukhc. Tubulin alpha chain. Chain: a. Tubulin beta chain. Chain: b. Synonym: beta tubulin
Source: Homo sapiens. Human. Other_details: the actual construct used in the em studies is a mutant protein (called cys-lite). Bos taurus. Bovine. Bovine
Authors: C.V.Sindelar,K.H.Downing
Key ref: C.V.Sindelar and K.H.Downing (2007). The beginning of kinesin's force-generating cycle visualized at 9-A resolution. J Cell Biol, 177, 377-385. PubMed id: 17470637 DOI: 10.1083/jcb.200612090
Date:
12-Mar-07     Release date:   08-Jul-08    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P33176  (KINH_HUMAN) -  Kinesin-1 heavy chain
Seq:
Struc: 		 
Seq:
Struc: 		963 a.a.
323 a.a.
Protein chain
No UniProt id for this chain
Protein chain
Pfam   ArchSchema ?
Q6B856  (TBB2B_BOVIN) -  Tubulin beta-2B chain
Seq:
Struc: 		445 a.a.
426 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure
* PDB and UniProt seqs differ at 4 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     protein complex   4 terms 
  Biological process     microtubule-based process   5 terms 
  Biochemical function     structural molecule activity     6 terms  

 

 
DOI no: 10.1083/jcb.200612090 J Cell Biol 177:377-385 (2007)
PubMed id: 17470637  
 
 
The beginning of kinesin's force-generating cycle visualized at 9-A resolution.
C.V.Sindelar, K.H.Downing.
 
  ABSTRACT  
 
We have used cryo-electron microscopy of kinesin-decorated microtubules to resolve the structure of the motor protein kinesin's crucial nucleotide response elements, switch I and the switch II helix, in kinesin's poorly understood nucleotide-free state. Both of the switch elements undergo conformational change relative to the microtubule-free state. The changes in switch I suggest a role for it in "ejecting" adenosine diphosphate when kinesin initially binds to the microtubule. The switch II helix has an N-terminal extension, apparently stabilized by conserved microtubule contacts, implying a microtubule activation mechanism that could convey the state of the bound nucleotide to kinesin's putative force-delivering element (the "neck linker"). In deriving this structure, we have adapted an image-processing technique, single-particle reconstruction, for analyzing decorated microtubules. The resulting reconstruction visualizes the asymmetric seam present in native, 13-protofilament microtubules, and this method will provide an avenue to higher-resolution characterization of a variety of microtubule- binding proteins, as well as the microtubule itself.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20935055 C.L.Lawson, M.L.Baker, C.Best, C.Bi, M.Dougherty, P.Feng, G.van Ginkel, B.Devkota, I.Lagerstedt, S.J.Ludtke, R.H.Newman, T.J.Oldfield, I.Rees, G.Sahni, R.Sala, S.Velankar, J.Warren, J.D.Westbrook, K.Henrick, G.J.Kleywegt, H.M.Berman, and W.Chiu (2011).
EMDataBank.org: unified data resource for CryoEM.
  Nucleic Acids Res, 39, D456-D464.  
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
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.  
20212149 D.S.Martin, R.Fathi, T.J.Mitchison, and J.Gelles (2010).
FRET measurements of kinesin neck orientation reveal a structural basis for processivity and asymmetry.
  Proc Natl Acad Sci U S A, 107, 5453-5458.  
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
20696402 H.Sui, and K.H.Downing (2010).
Structural basis of interprotofilament interaction and lateral deformation of microtubules.
  Structure, 18, 1022-1031.  
20025975 J.Cope, S.Gilbert, I.Rayment, D.Mastronarde, and A.Hoenger (2010).
Cryo-electron tomography of microtubule-kinesin motor complexes.
  J Struct Biol, 170, 257-265.  
20224548 S.Uchimura, Y.Oguchi, Y.Hachikubo, S.Ishiwata, and E.Muto (2010).
Key residues on microtubule responsible for activation of kinesin ATPase.
  EMBO J, 29, 1167-1175.  
19321748 A.B.Asenjo, and H.Sosa (2009).
A mobile kinesin-head intermediate during the ATP-waiting state.
  Proc Natl Acad Sci U S A, 106, 5657-5662.  
19506764 A.G.Larson, E.C.Landahl, and S.E.Rice (2009).
Mechanism of cooperative behaviour in systems of slow and fast molecular motors.
  Phys Chem Chem Phys, 11, 4890-4898.  
19530174 A.Marx, A.Hoenger, and E.Mandelkow (2009).
Structures of kinesin motor proteins.
  Cell Motil Cytoskeleton, 66, 958-966.  
19135893 J.C.Cochran, C.V.Sindelar, N.K.Mulko, K.A.Collins, S.E.Kong, R.S.Hawley, and F.J.Kull (2009).
ATPase cycle of the nonmotile kinesin NOD allows microtubule end tracking and drives chromosome movement.
  Cell, 136, 110-122.
PDB codes: 3dc4 3dcb 3dco
19935670 N.Hirokawa, R.Nitta, and Y.Okada (2009).
The mechanisms of kinesin motor motility: lessons from the monomeric motor KIF1A.
  Nat Rev Mol Cell Biol, 10, 877-884.  
19693012 N.R.Guydosh, and S.M.Block (2009).
Direct observation of the binding state of the kinesin head to the microtubule.
  Nature, 461, 125-128.  
21544223 V.Hariharan, and W.O.Hancock (2009).
Insights into the Mechanical Properties of the Kinesin Neck Linker Domain from Sequence Analysis and Molecular Dynamics Simulations.
  Cell Mol Bioeng, 2, 177-189.  
19452133 W.Hwang, and M.J.Lang (2009).
Mechanical design of translocating motor proteins.
  Cell Biochem Biophys, 54, 11-22.  
19348763 Y.L.Wong, K.A.Dietrich, N.Naber, R.Cooke, and S.E.Rice (2009).
The Kinesin-1 tail conformationally restricts the nucleotide pocket.
  Biophys J, 96, 2799-2807.  
19074350 A.P.Carter, J.E.Garbarino, E.M.Wilson-Kubalek, W.E.Shipley, C.Cho, R.A.Milligan, R.D.Vale, and I.R.Gibbons (2008).
Structure and functional role of dynein's microtubule-binding domain.
  Science, 322, 1691-1695.
PDB code: 3err
19047639 A.S.Khalil, D.C.Appleyard, A.K.Labno, A.Georges, M.Karplus, A.M.Belcher, W.Hwang, and M.J.Lang (2008).
Kinesin's cover-neck bundle folds forward to generate force.
  Proc Natl Acad Sci U S A, 105, 19247-19252.  
18294653 C.A.Moores, and R.A.Milligan (2008).
Visualisation of a kinesin-13 motor on microtubule end mimics.
  J Mol Biol, 377, 647-654.  
19000825 D.Tan, W.J.Rice, and H.Sosa (2008).
Structure of the kinesin13-microtubule ring complex.
  Structure, 16, 1732-1739.
PDB code: 3edl
18579780 K.A.Dietrich, C.V.Sindelar, P.D.Brewer, K.H.Downing, C.R.Cremo, and S.E.Rice (2008).
The kinesin-1 motor protein is regulated by a direct interaction of its head and tail.
  Proc Natl Acad Sci U S A, 105, 8938-8943.  
18280159 M.Kikkawa (2008).
The role of microtubules in processive kinesin movement.
  Trends Cell Biol, 18, 128-135.  
18806800 R.Nitta, Y.Okada, and N.Hirokawa (2008).
Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin.
  Nat Struct Mol Biol, 15, 1067-1075.
PDB codes: 2zfi 2zfj 2zfk 2zfl 2zfm
17989090 L.A.Amos, and K.Hirose (2007).
A cool look at the structural changes in kinesin motor domains.
  J Cell Sci, 120, 3919-3927.  
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.