5MLV

S. pombe microtubule decorated with Cut7 motor domain in the AMPPNP state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Cryo-EM Structure (4.5- angstrom ) of Yeast Kinesin-5-Microtubule Complex Reveals a Distinct Binding Footprint and Mechanism of Drug Resistance.

von Loeffelholz, O.Pena, A.Drummond, D.R.Cross, R.Moores, C.A.

(2019) J. Mol. Biol. 431: 864-872

  • DOI: 10.1016/j.jmb.2019.01.011

  • PubMed Abstract: 
  • Kinesin-5s are microtubule-dependent motors that drive spindle pole separation during mitosis. We used cryo-electron microscopy to determine the 4.5-Å resolution structure of the motor domain of the fission yeast kinesin-5 Cut7 bound to fission yeast ...

    Kinesin-5s are microtubule-dependent motors that drive spindle pole separation during mitosis. We used cryo-electron microscopy to determine the 4.5-Å resolution structure of the motor domain of the fission yeast kinesin-5 Cut7 bound to fission yeast microtubules and explored the topology of the motor-microtubule interface and the susceptibility of the complex to drug binding. Despite their non-canonical architecture and mechanochemistry, Schizosaccharomyces pombe microtubules were stabilized by epothilone at the taxane binding pocket. The overall Cut7 footprint on the S. pombe microtubule surface is altered compared to mammalian tubulin microtubules because of their different polymer architectures. However, the core motor-microtubule interaction is tightly conserved, reflected in similar Cut7 ATPase activities on each microtubule type. AMPPNP-bound Cut7 adopts a kinesin-conserved ATP-like conformation including cover neck bundle formation. However, the Cut7 ATPase is not blocked by a mammalian-specific kinesin-5 inhibitor, consistent with the non-conserved sequence and structure of its loop5 insertion.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK.,Division of Biomedical Cell Biology, Warwick Medical School, Coventry, CV4 7AL, UK.,Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK. Electronic address: c.moores@mail.cryst.bbk.ac.uk.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1 chain
E, M, B, H, K, Q
455Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: nda2
Find proteins for P04688 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P04688
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Kinesin-like protein cut7
G, O, A, D, J, P
432Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: cut7
Find proteins for P24339 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P24339
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
I, N, C, F, L, R
448Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: nda3 (alp12)
Find proteins for P05219 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  P05219
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
C, F, I, L, N, R
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
B, E, H, K, M, Q
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
ANP
Query on ANP

Download SDF File 
Download CCD File 
A, D, G, J, O, P
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
EPB
Query on EPB

Download SDF File 
Download CCD File 
C, F, I, L, N, R
7,11-DIHYDROXY-8,8,10,12,16-PENTAMETHYL-3-[1-METHYL-2-(2-METHYL-THIAZOL-4-YL)VINYL]-4,17-DIOXABICYCLO[14.1.0]HEPTADECANE-5,9-DIONE
EPOTHILONE B
C27 H41 N O6 S
QXRSDHAAWVKZLJ-PVYNADRNSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A, D, G, J, O, P
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.5 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 
Software Package:
Software NamePurpose
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Biotechnology and Biological Sciences Research CouncilUnited KingdomL00190X/1

Revision History 

  • Version 1.0: 2018-08-08
    Type: Initial release
  • Version 1.1: 2019-02-20
    Type: Advisory, Data collection, Database references, Derived calculations
  • Version 1.2: 2019-02-27
    Type: Data collection, Database references
  • Version 1.3: 2019-12-11
    Type: Other