5MJS

S. pombe microtubule copolymerized with GTP and Mal3-143


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.6 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Nucleotide- and Mal3-dependent changes in fission yeast microtubules suggest a structural plasticity view of dynamics.

von Loeffelholz, O.Venables, N.A.Drummond, D.R.Katsuki, M.Cross, R.Moores, C.A.

(2017) Nat Commun 8: 2110-2110

  • DOI: 10.1038/s41467-017-02241-5

  • PubMed Abstract: 
  • Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assemb ...

    Using cryo-electron microscopy, we characterize the architecture of microtubules assembled from Schizosaccharomyces pombe tubulin, in the presence and absence of their regulatory partner Mal3. Cryo-electron tomography reveals that microtubules assembled from S. pombe tubulin have predominantly B-lattice interprotofilament contacts, with protofilaments skewed around the microtubule axis. Copolymerization with Mal3 favors 13 protofilament microtubules with reduced protofilament skew, indicating that Mal3 adjusts interprotofilament interfaces. A 4.6-Å resolution structure of microtubule-bound Mal3 shows that Mal3 makes a distinctive footprint on the S. pombe microtubule lattice and that unlike mammalian microtubules, S. pombe microtubules do not show the longitudinal lattice compaction associated with EB protein binding and GTP hydrolysis. Our results firmly support a structural plasticity view of microtubule dynamics in which microtubule lattice conformation is sensitive to a variety of effectors and differently so for different tubulins.


    Organizational Affiliation

    Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK.,Centre for Promotion of International Education and Research, Faculty of Agriculture, Kyushu University, Fukuoka, 812-8581, Japan.,CRUK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester, M20 4BX, UK.,Centre for Integrative Biology, Department of Integrated Structural Biology, Institute of Genetics and of Molecular and Cellular Biology, 1 rue Laurent Fries, Illkirch, France.,Department of Earth System Science, Faculty of Science, Fukuoka University, Fukuoka, 814-0180, Japan.,Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX, UK. c.moores@mail.cryst.bbk.ac.uk.,Division of Biomedical Cell Biology, Warwick Medical School, CV4 7AL, Coventry, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Tubulin beta chain
A, J, B, C
429Schizosaccharomyces 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
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Microtubule integrity protein mal3
D
143Schizosaccharomyces pombe (strain 972 / ATCC 24843)Mutation(s): 0 
Gene Names: mal3
Find proteins for Q10113 (Schizosaccharomyces pombe (strain 972 / ATCC 24843))
Go to UniProtKB:  Q10113
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Tubulin alpha-1 chain
E, F, G, H
444Schizosaccharomyces 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
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP

Download SDF File 
Download CCD File 
A, B, C, J
GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N
 Ligand Interaction
GTP
Query on GTP

Download SDF File 
Download CCD File 
E, F, G, H
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.6 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 KingdomBB/L00190X/1

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2019-10-23
    Type: Data collection, Other