Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 3-mer - A2B1 

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

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 157.88 kDa 
• Atom Count: 9076 
• Modelled Residue Count: 1134 
• Deposited Residue Count: 1397 
• Unique protein chains: 3

5ND3

Microtubule-bound MKLP2 motor domain in the with no nucleotide

• PDB DOI: 10.2210/pdb5ND3/pdb
• EM Map EMD-3621:EMDBEMDataResource

• Classification: MOTOR PROTEIN
• Organism(s): Mus musculus, Bos taurus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-03-07 Released: 2017-10-04 
• Deposition Author(s): Atherton, J., Yu, I.M., Cook, A., Muretta, J.M., Joseph, A.P., Major, J., Sourigues, Y., Clause, J., Topf, M., Rosenfeld, S.S., Houdusse, A., Moores, C.A.
• Funding Organization(s): Medical Research Council (United Kingdom), American Heart Association, National Institutes of Health, CNRS, Instruct-pilote, Ligue Contre le Cancer, ARC, INCa, Marie Curie Fellowship, Labex CelTisPhyBio, PSL Research University

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Literature

The divergent mitotic kinesin MKLP2 exhibits atypical structure and mechanochemistry.

Atherton, J., Yu, I.M., Cook, A., Muretta, J.M., Joseph, A., Major, J., Sourigues, Y., Clause, J., Topf, M., Rosenfeld, S.S., Houdusse, A., Moores, C.A.

(2017) Elife 6

• PubMed: 28826477 
• DOI: 10.7554/eLife.27793
• Primary Citation of Related Structures:  
  5ND2, 5ND3, 5ND4, 5ND7


• PubMed Abstract: 
  

MKLP2, a kinesin-6, has critical roles during the metaphase-anaphase transition and cytokinesis. Its motor domain contains conserved nucleotide binding motifs, but is divergent in sequence (~35% identity) and size (~40% larger) compared to other kinesins. Using cryo-electron microscopy and biophysical assays, we have undertaken a mechanochemical dissection of the microtubule-bound MKLP2 motor domain during its ATPase cycle, and show that many facets of its mechanism are distinct from other kinesins. While the MKLP2 neck-linker is directed towards the microtubule plus-end in an ATP-like state, it does not fully dock along the motor domain. Furthermore, the footprint of the MKLP2 motor domain on the MT surface is altered compared to motile kinesins, and enhanced by kinesin-6-specific sequences. The conformation of the highly extended loop6 insertion characteristic of kinesin-6s is nucleotide-independent and does not contact the MT surface. Our results emphasize the role of family-specific insertions in modulating kinesin motor function.

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Organizational Affiliation: 

Institute of Structural and Molecular Biology, Birkbeck College, London, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Kinesin-like protein KIF20A	A [auth C]	501	Mus musculus	Mutation(s): 0  Gene Names: Kif20a, Rab6kifl
UniProt & NIH Common Fund Data Resources
Find proteins for P97329 (Mus musculus) Explore P97329  Go to UniProtKB:  P97329
IMPC:  MGI:1201682

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha chain	B [auth A]	451	Bos taurus	Mutation(s): 0
UniProt
Find proteins for P81947 (Bos taurus) Explore P81947  Go to UniProtKB:  P81947

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta-2B chain	C [auth B]	445	Bos taurus	Mutation(s): 0  Gene Names: TUBB2B
UniProt
Find proteins for Q6B856 (Bos taurus) Explore Q6B856  Go to UniProtKB:  Q6B856

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA1	G [auth B]	TAXOL C47 H51 N O14 RCINICONZNJXQF-MZXODVADSA-N
GTP	D [auth A]	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	F [auth B]	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	E [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
TA1	BindingDB:  5ND3	EC50: 520 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-03-07 
• Released Date: 2017-10-04 
Deposition Author(s): Atherton, J., Yu, I.M., Cook, A., Muretta, J.M., Joseph, A.P., Major, J., Sourigues, Y., Clause, J., Topf, M., Rosenfeld, S.S., Houdusse, A., Moores, C.A.

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Funding Organization	Location	Grant Number
Medical Research Council (United Kingdom)	United Kingdom	MR/J000973/1
Medical Research Council (United Kingdom)	United Kingdom	MR/J003867/1
Medical Research Council (United Kingdom)	United Kingdom	MR/M019292/1
American Heart Association	United States	SDG20480032
National Institutes of Health	United States	GM102875
National Institutes of Health	United States	NS073610
CNRS		ANR-15-CE13-0017-01
Instruct-pilote, Ligue Contre le Cancer		RS14/75-28
ARC		PJA 20151203285
INCa		2016-1-PL BIO-10-ICR-1
Marie Curie Fellowship		FP7-PEOPLE-2012-IIF
Labex CelTisPhyBio		11-LBX-0038
PSL Research University		ANR-10-IDEX-0001-02 PSL

Revision History  

• Version 1.0: 2017-10-04
  Type: Initial release