3J8Y

High-resolution structure of ATP analog-bound kinesin on microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

High-resolution structures of kinesin on microtubules provide a basis for nucleotide-gated force-generation.

Shang, Z.Zhou, K.Xu, C.Csencsits, R.Cochran, J.C.Sindelar, C.V.

(2014) Elife 3: e04686-e04686

  • DOI: 10.7554/eLife.04686
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing atomic models for no-nucleotide and ATP states of the mo ...

    Microtubule-based transport by the kinesin motors, powered by ATP hydrolysis, is essential for a wide range of vital processes in eukaryotes. We obtained insight into this process by developing atomic models for no-nucleotide and ATP states of the monomeric kinesin motor domain on microtubules from cryo-EM reconstructions at 5-6 Å resolution. By comparing these models with existing X-ray structures of ADP-bound kinesin, we infer a mechanistic scheme in which microtubule attachment, mediated by a universally conserved 'linchpin' residue in kinesin (N255), triggers a clamshell opening of the nucleotide cleft and accompanying release of ADP. Binding of ATP re-closes the cleft in a manner that tightly couples to translocation of cargo, via kinesin's 'neck linker' element. These structural transitions are reminiscent of the analogous nucleotide-exchange steps in the myosin and F1-ATPase motors and inform how the two heads of a kinesin dimer 'gate' each other to promote coordinated stepping along microtubules.


    Organizational Affiliation

    Department of Biology, Brandeis University, Waltham, United States.,Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, United States.,Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, United States.,Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Kinesin-1 heavy chain
K
349Homo sapiensMutation(s): 0 
Gene Names: KIF5B (KNS, KNS1)
Find proteins for P33176 (Homo sapiens)
Go to Gene View: KIF5B
Go to UniProtKB:  P33176
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1B chain
A
451Sus scrofaMutation(s): 0 
Gene Names: TUBA1B
Find proteins for Q2XVP4 (Sus scrofa)
Go to Gene View: TUBA1B
Go to UniProtKB:  Q2XVP4
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta-2B chain
B
445Sus scrofaMutation(s): 0 
Gene Names: TUBB
Find proteins for F2Z5B2 (Sus scrofa)
Go to Gene View: TUBB
Go to UniProtKB:  F2Z5B2
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
ATP
Query on ATP

Download SDF File 
Download CCD File 
K
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
K
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-10
    Type: Initial release
  • Version 1.1: 2015-06-03
    Type: Database references
  • Version 1.2: 2018-07-18
    Type: Author supporting evidence, Data collection