5FLZ

Cryo-EM structure of gamma-TuSC oligomers in a closed conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structure of Gamma-Tubulin Small Complex Based on a Cryo-Em Map, Chemical Cross-Links, and a Remotely Related Structure.

Greenberg, C.H.Kollman, J.Zelter, A.Johnson, R.Maccoss, M.J.Davis, T.N.Agard, D.A.Sali, A.

(2016) J Struct Biol 194: 303

  • DOI: 10.1016/j.jsb.2016.03.006
  • Primary Citation of Related Structures:  
    5FLZ, 5FM1

  • PubMed Abstract: 
  • Modeling protein complex structures based on distantly related homologues can be challenging due to poor sequence and structure conservation. Therefore, utilizing even low-resolution experimental data can significantly increase model precision and accuracy ...

    Modeling protein complex structures based on distantly related homologues can be challenging due to poor sequence and structure conservation. Therefore, utilizing even low-resolution experimental data can significantly increase model precision and accuracy. Here, we present models of the two key functional states of the yeast γ-tubulin small complex (γTuSC): one for the low-activity "open" state and another for the higher-activity "closed" state. Both models were computed based on remotely related template structures and cryo-EM density maps at 6.9Å and 8.0Å resolution, respectively. For each state, extensive sampling of alignments and conformations was guided by the fit to the corresponding cryo-EM density map. The resulting good-scoring models formed a tightly clustered ensemble of conformations in most regions. We found significant structural differences between the two states, primarily in the γ-tubulin subunit regions where the microtubule binds. We also report a set of chemical cross-links that were found to be consistent with equilibrium between the open and closed states. The protocols developed here have been incorporated into our open-source Integrative Modeling Platform (IMP) software package (http://integrativemodeling.org), and can therefore be applied to many other systems.


    Related Citations: 
    • Ring Closure Activates Yeast Gamma-Turc for Species-Specific Microtubule Nucleation.
      Kollman, J.M., Greenberg, C.H., Li, S., Moritz, M., Zelter, A., Fong, K.K., Fernandez, J., Sali, A., Kilmartin, J., Davis, T.N., Agard, D.A.
      (2015) Nat Struct Mol Biol 22: 132

    Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, Department of Pharmaceutical Chemistry, California Institute for Quantitative Biosciences, University of California at San Francisco, San Francisco, CA, USA. Electronic address: sali@salilab.org.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SPINDLE POLE BODY COMPONENT SPC97A823Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P38863 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P38863 
Go to UniProtKB:  P38863
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SPINDLE POLE BODY COMPONENT SPC98B846Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for P53540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53540 
Go to UniProtKB:  P53540
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
TUBULIN GAMMA CHAINC, D473Saccharomyces cerevisiaeMutation(s): 2 
UniProt
Find proteins for P53378 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53378 
Go to UniProtKB:  P53378
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
SPINDLE POLE BODY COMPONENT 110E, F44Saccharomyces cerevisiaeMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.90 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2016-03-23
    Changes: Database references, Other
  • Version 1.2: 2016-05-11
    Changes: Database references, Other
  • Version 1.3: 2017-08-02
    Changes: Data collection