3KIN | pdb_00003kin

KINESIN (DIMERIC) FROM RATTUS NORVEGICUS

• PDB DOI: https://doi.org/10.2210/pdb3KIN/pdb

• Classification: MOTOR PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 1997-08-25 Released: 1998-10-14 
• Deposition Author(s): Kozielski, F., Sack, S., Marx, A., Thormahlen, M., Schonbrunn, E., Biou, V., Thompson, A., Mandelkow, E.-M., Mandelkow, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.362 (Depositor) 
• R-Value Observed: 
  0.289 (Depositor) 

Literature

The crystal structure of dimeric kinesin and implications for microtubule-dependent motility.

Kozielski, F., Sack, S., Marx, A., Thormahlen, M., Schonbrunn, E., Biou, V., Thompson, A., Mandelkow, E.M., Mandelkow, E.

(1997) Cell 91: 985-994

• PubMed: 9428521 
• DOI: https://doi.org/10.1016/s0092-8674(00)80489-4
• Primary Citation Related Structures: 
  3KIN


• PubMed Abstract: 
  

  The dimeric form of the kinesin motor and neck domain from rat brain with bound ADP has been solved by X-ray crystallography. The two heads of the dimer are connected via a coiled-coil alpha-helical interaction of their necks. They are broadly similar to one another; differences are most apparent in the head-neck junction and in a moderate reorientation of the neck helices in order to adopt to the coiled-coil conformation. The heads show a rotational symmetry (approximately 120 degrees) about an axis close to that of the coiled-coil. This arrangement is unexpected since it is not compatible with the microtubule lattice. In this arrangement, the two heads of a kinesin dimer could not have equivalent interactions with microtubules.

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Organizational Affiliation: 
• Max-Planck-Unit for Structural Molecular Biology, Hamburg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 81.5 kDa 
• Atom Count: 5,743 
• Modeled Residue Count: 708 
• Deposited Residue Count: 710 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN HEAVY CHAIN	A, C	238	Rattus norvegicus	Mutation(s): 0  EC: 3.6.4
UniProt
Find proteins for P56536 (Rattus norvegicus) Explore P56536  Go to UniProtKB:  P56536

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
KINESIN HEAVY CHAIN	B, D	117	Rattus norvegicus	Mutation(s): 0  EC: 5.6.1.3
UniProt
Find proteins for Q6QLM7 (Rattus norvegicus) Explore Q6QLM7  Go to UniProtKB:  Q6QLM7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ADP	E [auth A], F [auth C]	ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.362 (Depositor) 
• R-Value Observed: 0.289 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 72.15	α = 90
b = 91.85	β = 90
c = 141.68	γ = 90

Software Package:

Software Name	Purpose
PHASES	phasing
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 1998-10-14 
Deposition Author(s): Kozielski, F., Sack, S., Marx, A., Thormahlen, M., Schonbrunn, E., Biou, V., Thompson, A., Mandelkow, E.-M., Mandelkow, E.

Revision History  

• Version 1.0: 1998-10-14
  Type: Initial release
  
• Version 1.1: 2008-03-25
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2024-12-25
  Changes: Advisory, Data collection, Database references, Derived calculations, Structure summary