5MLV

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 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

Re-refinement Note

A newer entry is available that reflects an alternative modeling of the original data: 6S8M


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
  • Primary Citation of Related Structures:  
    5MLV

  • 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 microtubules and explored the topology of the motor-microtubule interface and the susceptibility of the complex to drug binding ...

    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. Electronic address: c.moores@mail.cryst.bbk.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1 chainJ [auth B], A [auth E], K [auth H], L [auth K], I [auth M], M [auth Q]455Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: nda2SPBC16A3.15c
UniProt
Find proteins for P04688 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P04688 
Go to UniProtKB:  P04688
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Kinesin-like protein cut7E [auth A], F [auth D], B [auth G], G [auth J], D [auth O], H [auth P]432Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: cut7SPAC25G10.07c
UniProt
Find proteins for P24339 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P24339 
Go to UniProtKB:  P24339
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainO [auth C], P [auth F], C [auth I], Q [auth L], N, R448Schizosaccharomyces pombe 972h-Mutation(s): 0 
Gene Names: nda3alp12SPBC26H8.07c
UniProt
Find proteins for P05219 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Explore P05219 
Go to UniProtKB:  P05219
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP (Subject of Investigation/LOI)
Query on GTP

Download Ideal Coordinates CCD File 
HA [auth M], IA [auth B], JA [auth H], KA [auth K], LA [auth Q], S [auth E]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
EPB (Subject of Investigation/LOI)
Query on EPB

Download Ideal Coordinates CCD File 
NA [auth N], PA [auth C], RA [auth F], TA [auth L], VA [auth R], W [auth I]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
C27 H41 N O6 S
QXRSDHAAWVKZLJ-PVYNADRNSA-N
 Ligand Interaction
ANP (Subject of Investigation/LOI)
Query on ANP

Download Ideal Coordinates CCD File 
AA [auth A], CA [auth D], EA [auth J], GA [auth P], U [auth G], Y [auth O]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
 Ligand Interaction
GDP (Subject of Investigation/LOI)
Query on GDP

Download Ideal Coordinates CCD File 
MA [auth N], OA [auth C], QA [auth F], SA [auth L], UA [auth R], V [auth I]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
BA [auth D], DA [auth J], FA [auth P], T [auth G], X [auth O], Z [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.50 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


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

Revision History  (Full details and data files)

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