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 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