4HNA

Kinesin motor domain in the ADP-MG-ALFX state in complex with tubulin and a DARPIN


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of a kinesin-tubulin complex and implications for kinesin motility.

Gigant, B.Wang, W.Dreier, B.Jiang, Q.Pecqueur, L.Pluckthun, A.Wang, C.Knossow, M.

(2013) Nat.Struct.Mol.Biol. 20: 1001-1007

  • DOI: 10.1038/nsmb.2624

  • PubMed Abstract: 
  • The typical function of kinesins is to transport cargo along microtubules. Binding of ATP to microtubule-attached motile kinesins leads to cargo displacement. To better understand the nature of the conformational changes that lead to the power stroke ...

    The typical function of kinesins is to transport cargo along microtubules. Binding of ATP to microtubule-attached motile kinesins leads to cargo displacement. To better understand the nature of the conformational changes that lead to the power stroke that moves a kinesin's load along a microtubule, we determined the X-ray structure of human kinesin-1 bound to αβ-tubulin. The structure defines the mechanism of microtubule-stimulated ATP hydrolysis, which releases the kinesin motor domain from microtubules. It also reveals the structural linkages that connect the ATP nucleotide to the kinesin neck linker, a 15-amino acid segment C terminal to the catalytic core of the motor domain, to result in the power stroke. ATP binding to the microtubule-bound kinesin favors neck-linker docking. This biases the attachment of kinesin's second head in the direction of the movement, thus initiating each of the steps taken.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales, Centre de Recherche de Gif, Centre National de la Recherche Scientifique, Gif sur Yvette, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha chain
A
451Ovis ariesMutation(s): 0 
Find proteins for D0VWZ0 (Ovis aries)
Go to UniProtKB:  D0VWZ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
B
445Ovis ariesMutation(s): 0 
Find proteins for D0VWY9 (Ovis aries)
Go to UniProtKB:  D0VWY9
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2
D
169N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
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
Small Molecules
Ligands 5 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
ADP
Query on ADP

Download SDF File 
Download CCD File 
K
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-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
ALF
Query on ALF

Download SDF File 
Download CCD File 
B, K
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J
 Ligand Interaction
MG
Query on MG

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.19 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.177 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 77.050α = 90.00
b = 160.540β = 90.00
c = 174.950γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
XSCALEdata scaling
SAWAYAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-12
    Type: Initial release
  • Version 1.1: 2013-08-21
    Type: Database references
  • Version 1.2: 2017-11-15
    Type: Source and taxonomy