Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A1B1C1D1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 157.23 kDa 
• Atom Count: 11209 
• Residue Count: 1331 
• Unique protein chains: 4

4LNU

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

• DOI: 10.2210/pdb4LNU/pdb

• Classification: CELL CYCLE/MOTOR PROTEIN
• Organism(s): Ovis aries, synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2013-07-12 Released: 2014-12-03 
• Deposition Author(s): Cao, L., Gigant, B., Knossow, M.

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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 

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

• PubMed: 25395082 
• 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 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.

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	A	451	Ovis aries	Mutation(s): 0  Gene Names: TUBA1B
Find proteins for W5QC38 (Ovis aries) Explore W5QC38  Go to UniProtKB:  W5QC38

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B	445	Ovis aries	Mutation(s): 0
Find proteins for D0VWY9 (Ovis aries) Explore D0VWY9  Go to UniProtKB:  D0VWY9

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Designed ankyrin repeat protein (DARPIN) D1	D	169	synthetic construct	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-1 heavy chain	K	325	Homo sapiens	Mutation(s): 5  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

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GTP	A	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MES	B	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
SO4	A, B, K	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	B, D, K	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

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 = 73.4	α = 116.16
b = 83.01	β = 105.08
c = 83.307	γ = 97.57

Software Package:

Software Name	Purpose
PHASER	phasing
BUSTER	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-07-12 
• Released Date: 2014-12-03 
Deposition Author(s): Cao, L., Gigant, B., Knossow, M.

Revision History 

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