Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: microscopy

Macromolecule Content

• Total Structure Weight: 102.79 kDa 
• Atom Count: 6913 
• Residue Count: 867 
• Unique protein chains: 2

5W3J

Yeast microtubule stabilized with Taxol assembled from mutated tubulin

• DOI: 10.2210/pdb5W3J/pdb
• EMDataResource: EMD-8757

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae S288C
• Expression System: Saccharomyces cerevisiae S288C
• Mutation(s): Yes 


• Deposited: 2017-06-07 Released: 2017-07-19 
• Deposition Author(s): Howes, S.C., Geyer, E.A., LaFrance, B., Zhang, R., Kellogg, E.H., Westermann, S., Rice, L.M., Nogales, E.
• Funding Organization(s): National Science Foundation (NSF, United States), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

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

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

• PubMed: 28652389 
• DOI: 10.1083/jcb.201612195
• Primary Citation of Related Structures:  
  5W3J, 5W3F, 5W3H


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin alpha-1 chain	A	447	Saccharomyces cerevisiae S288C	Mutation(s): 0  Gene Names: TUB1, YML085C
Find proteins for P09733 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P09733  Go to UniProtKB:  P09733

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tubulin beta chain	B	457	Saccharomyces cerevisiae S288C	Mutation(s): 5  Gene Names: TUB2, YFL037W
Find proteins for P02557 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02557  Go to UniProtKB:  P02557

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
TA1	B	TAXOL C47 H51 N O14 RCINICONZNJXQF-MZXODVADSA-N
GTP	A	GUANOSINE-5'-TRIPHOSPHATE C10 H16 N5 O14 P3 XKMLYUALXHKNFT-UUOKFMHZSA-N
GDP	B	GUANOSINE-5'-DIPHOSPHATE C10 H15 N5 O11 P2 QGWNDRXFNXRZMB-UUOKFMHZSA-N
MG	A	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2017-06-07 
• Released Date: 2017-07-19 
Deposition Author(s): Howes, S.C., Geyer, E.A., LaFrance, B., Zhang, R., Kellogg, E.H., Westermann, S., Rice, L.M., Nogales, E.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	1106400
National Science Foundation (NSF, United States)	United States	MCB 1054947
National Science Foundation (NSF, United States)	United States	1615938
National Science Foundation (NSF, United States)	United States	2014177758
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01-GM098543
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	T32-GM008297
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01-GM051487

Revision History 

• 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