5FLZ

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.9 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:  

  • 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 ac ...

    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: cgreen@salilab.org.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SPINDLE POLE BODY COMPONENT SPC97
A
823Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPC97
Find proteins for P38863 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P38863
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
SPINDLE POLE BODY COMPONENT SPC98
B
846Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: SPC98
Find proteins for P53540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53540
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
TUBULIN GAMMA CHAIN
C, D
473Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 2 
Gene Names: TUB4
Find proteins for P53378 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P53378
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
SPINDLE POLE BODY COMPONENT 110
E, F
44N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
UNK
Query on UNK
E, F
L-PEPTIDE LINKINGC4 H9 N O2

--

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.9 Å
  • Aggregation State: FILAMENT 
  • Reconstruction Method: HELICAL 

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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