5MM7

Ustilago maydis kinesin-5 motor domain with N-terminal extension in the AMPPNP state bound to microtubules


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Cryo-EM structure of the Ustilago maydis kinesin-5 motor domain bound to microtubules.

von Loeffelholz, O.Ann Moores, C.

(2019) J Struct Biol 

  • DOI: https://doi.org/10.1016/j.jsb.2019.07.003
  • Primary Citation of Related Structures:  
    5MM4, 5MM7

  • PubMed Abstract: 

    In many eukaryotes, kinesin-5 motors are essential for mitosis, and small molecules that inhibit human kinesin-5 disrupt cell division. To investigate whether fungal kinesin-5s could be targets for novel fungicides, we studied kinesin-5 from the pathogenic fungus Ustilago maydis. We used cryo-electron microscopy to determine the microtubule-bound structure of its motor domain with and without the N-terminal extension. The ATP-like conformations of the motor in the presence or absence of this N-terminus are very similar, suggesting this region is structurally disordered and does not directly influence the motor ATPase. The Ustilago maydis kinesin-5 motor domain adopts a canonical ATP-like conformation, thereby allowing the neck linker to bind along the motor domain towards the microtubule plus end. However, several insertions within this motor domain are structurally distinct. Loop2 forms a non-canonical interaction with α-tubulin, while loop8 may bridge between two adjacent protofilaments. Furthermore, loop5 - which in human kinesin-5 is involved in binding allosteric inhibitors - protrudes above the nucleotide binding site, revealing a distinct binding pocket for potential inhibitors. This work highlights fungal-specific elaborations of the kinesin-5 motor domain and provides the structural basis for future investigations of kinesins as targets for novel fungicides.


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, London WC1E 7HX, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
kinesin-5A [auth K]457Ustilago maydisMutation(s): 0 
Gene Names: UMAG_10678
UniProt
Find proteins for A0A0D1DQH0 (Ustilago maydis (strain 521 / FGSC 9021))
Explore A0A0D1DQH0 
Go to UniProtKB:  A0A0D1DQH0
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A0D1DQH0
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin alpha-1A chainB [auth A]439Sus scrofaMutation(s): 0 
Gene Names: TUBA1A
UniProt
Find proteins for P02550 (Sus scrofa)
Explore P02550 
Go to UniProtKB:  P02550
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02550
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Tubulin beta chainC [auth B]427Sus scrofaMutation(s): 0 
UniProt
Find proteins for P02554 (Sus scrofa)
Explore P02554 
Go to UniProtKB:  P02554
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02554
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1

Download Ideal Coordinates CCD File 
H [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N
GTP
Query on GTP

Download Ideal Coordinates CCD File 
F [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
ANP
Query on ANP

Download Ideal Coordinates CCD File 
E [auth K]PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
C10 H17 N6 O12 P3
PVKSNHVPLWYQGJ-KQYNXXCUSA-N
GDP
Query on GDP

Download Ideal Coordinates CCD File 
I [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth K],
G [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
TA1 BindingDB:  5MM7 EC50: 520 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.10 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: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-11
    Changes: Other