5W3J

Yeast microtubule stabilized with Taxol assembled from mutated tubulin

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.6 of the entry. See complete history. 


Literature

Structural differences between yeast and mammalian microtubules revealed by cryo-EM.

Howes, S.C., Geyer, E.A., LaFrance, B., Zhang, R., Kellogg, E.H., Westermann, S., Rice, L.M., Nogales, E.

(2017) J Cell Biol 216: 2669-2677

  • DOI: 10.1083/jcb.201612195
  • Primary Citation of Related Structures:  
    5W3F, 5W3H, 5W3J

  • PubMed Abstract: 

    • Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis ...

    Microtubules are polymers of αβ-tubulin heterodimers essential for all eukaryotes. Despite sequence conservation, there are significant structural differences between microtubules assembled in vitro from mammalian or budding yeast tubulin. Yeast MTs were not observed to undergo compaction at the interdimer interface as seen for mammalian microtubules upon GTP hydrolysis. Lack of compaction might reflect slower GTP hydrolysis or a different degree of allosteric coupling in the lattice. The microtubule plus end-tracking protein Bim1 binds yeast microtubules both between αβ-tubulin heterodimers, as seen for other organisms, and within tubulin dimers, but binds mammalian tubulin only at interdimer contacts. At the concentrations used in cryo-electron microscopy, Bim1 causes the compaction of yeast microtubules and induces their rapid disassembly. Our studies demonstrate structural differences between yeast and mammalian microtubules that likely underlie their differing polymerization dynamics. These differences may reflect adaptations to the demands of different cell size or range of physiological growth temperatures.

    Organizational Affiliation: 

    Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin alpha-1 chainA447Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: TUB1, YML085C
UniProt
Find proteins for P09733 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P09733 
Go to UniProtKB:  P09733
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP09733
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Tubulin beta chainB457Saccharomyces cerevisiae S288CMutation(s): 5 
Gene Names: TUB2, YFL037W
UniProt
Find proteins for P02557 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02557 
Go to UniProtKB:  P02557
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02557
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TA1
Query on TA1
Download Ideal Coordinates CCD File 
F [auth B]TAXOL
C47 H51 N O14
RCINICONZNJXQF-MZXODVADSA-N		 Ligand Interaction
GTP
Query on GTP
Download Ideal Coordinates CCD File 
C [auth A]GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N		 Ligand Interaction
GDP
Query on GDP
Download Ideal Coordinates CCD File 
E [auth B]GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
D [auth A]MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: HELICAL ARRAY 
  • Reconstruction Method: HELICAL 

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Science Foundation (NSF, United States)United States1106400
National Science Foundation (NSF, United States)United StatesMCB 1054947
National Science Foundation (NSF, United States)United States1615938
National Science Foundation (NSF, United States)United States2014177758
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM098543
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32-GM008297
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01-GM051487

Revision History  (Full details and data files)

  • Version 1.0: 2017-07-19
    Type: Initial release
  • Version 1.1: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references
  • Version 1.2: 2017-11-08
    Changes: Derived calculations
  • Version 1.3: 2018-08-15
    Changes: Data collection, Other
  • Version 1.4: 2018-08-29
    Changes: Data collection, Source and taxonomy, Structure summary
  • Version 1.5: 2019-11-27
    Changes: Author supporting evidence
  • Version 1.6: 2019-12-18
    Changes: Other