4LNU

Nucleotide-free kinesin motor domain in complex with tubulin and a DARPin


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 

wwPDB Validation   3D Report Full Report



Literature

The structure of apo-kinesin bound to tubulin links the nucleotide cycle to movement

Cao, L.Wang, W.Jiang, Q.Wang, C.Knossow, M.Gigant, B.

(2014) Nat Commun 5: 5364-5364

  • DOI: 10.1038/ncomms6364
  • Primary Citation of Related Structures:  
    4LNU

  • PubMed Abstract: 
  • Kinesin-1 is a dimeric ATP-dependent motor protein that moves towards microtubules (+) ends. This movement is driven by two conformations (docked and undocked) of the two motor domains carboxy-terminal peptides (named neck linkers), in correlation with t ...

    Kinesin-1 is a dimeric ATP-dependent motor protein that moves towards microtubules (+) ends. This movement is driven by two conformations (docked and undocked) of the two motor domains carboxy-terminal peptides (named neck linkers), in correlation with the nucleotide bound to each motor domain. Despite extensive data on kinesin-1, the structural connection between its nucleotide cycle and movement has remained elusive, mostly because the structure of the critical tubulin-bound apo-kinesin state was unknown. Here we report the 2.2 Å structure of this complex. From its comparison with detached kinesin-ADP and tubulin-bound kinesin-ATP, we identify three kinesin motor subdomains that move rigidly along the nucleotide cycle. Our data reveal how these subdomains reorient on binding to tubulin and when ATP binds, leading respectively to ADP release and to neck linker docking. These results establish a framework for understanding the transformation of chemical energy into mechanical work by (+) end-directed kinesins.


    Organizational Affiliation

    Laboratoire d'Enzymologie et Biochimie Structurales (LEBS), Centre de Recherche de Gif, Centre National de la Recherche Scientifique, 1 avenue de la Terrasse, 91190 Gif sur Yvette, France.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha chain A451Ovis ariesMutation(s): 0 
Gene Names: TUBA1B
Find proteins for W5QC38 (Ovis aries)
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Go to UniProtKB:  W5QC38
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
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Designed ankyrin repeat protein (DARPIN) D1 D169synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-1 heavy chain K325Homo sapiensMutation(s): 5 
Gene Names: KIF5BKNSKNS1
Find proteins for P33176 (Homo sapiens)
Explore P33176 
Go to UniProtKB:  P33176
NIH Common Fund Data Resources
PHAROS:  P33176
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 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

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B
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MES
Query on MES

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B
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
C6 H13 N O4 S
SXGZJKUKBWWHRA-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, K
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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B, D, K
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

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A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.19 Å
  • R-Value Free: 0.195 
  • R-Value Work: 0.155 
  • R-Value Observed: 0.157 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 73.4α = 116.16
b = 83.01β = 105.08
c = 83.307γ = 97.57
Software Package:
Software NamePurpose
PHASERphasing
BUSTERrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-12-03
    Type: Initial release