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 
  • R-Value Observed: 0.178 

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
  • Primary Citation of Related Structures:  
    4HNA

  • 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 tha ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chain A451Ovis ariesMutation(s): 0 
Find proteins for D0VWZ0 (Ovis aries)
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Go to UniProtKB:  D0VWZ0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chain B445Ovis ariesMutation(s): 0 
Find proteins for D0VWY9 (Ovis aries)
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Go to UniProtKB:  D0VWY9
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
DESIGNED ANKYRIN REPEAT PROTEIN (DARPIN) D2 D169synthetic constructMutation(s): 0 
Protein Feature View
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-1 heavy chain K349Homo sapiensMutation(s): 0 
Gene Names: KIF5B, KNS, KNS1
Find proteins for P33176 (Homo sapiens)
Explore P33176 
Go to UniProtKB:  P33176
NIH Common Fund Data Resources
PHAROS:  P33176
GTEx:  ENSG00000170759
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP
Download Ideal Coordinates CCD File 
A
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
ADP
Query on ADP
Download Ideal Coordinates CCD File 
K
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N		 Ligand Interaction
ALF
Query on ALF
Download Ideal Coordinates CCD File 
B, K
TETRAFLUOROALUMINATE ION
Al F4
UYOMQIYKOOHAMK-UHFFFAOYSA-J		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates 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 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.05α = 90
b = 160.54β = 90
c = 174.95γ = 90
Software Package:
Software NamePurpose
AMoREphasing
BUSTERrefinement
XDSdata reduction
XSCALEdata scaling
SAWAYAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

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