Biological Assembly 1  

 3D View: Structure | Validation Report

Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 42-mer - A14B14C14 Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 42-mer - A14B14C7D7 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 308.27 kDa 
• Atom Count: 16942 
• Modelled Residue Count: 2118 
• Deposited Residue Count: 2703 
• Unique protein chains: 4

5FLZ

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

• DOI: 10.2210/pdb5FLZ/pdb
• EMDataResource: EMD-2799

• Classification: CELL CYCLE
• Organism(s): Saccharomyces cerevisiae
• Expression System: unidentified baculovirus
• Mutation(s): Yes 


• Deposited: 2015-10-29 Released: 2016-01-13 
• Deposition Author(s): Greenberg, C.H., Kollman, J., Zelter, A., Johnson, R., MacCoss, M.J., Davis, T.N., Agard, D.A., Sali, A.

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Experimental Data Snapshot

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

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

• PubMed: 26968363 
• 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. 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.

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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

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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: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE POLE BODY COMPONENT SPC97	A	823	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P38863 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P38863  Go to UniProtKB:  P38863

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE POLE BODY COMPONENT SPC98	B	846	Saccharomyces cerevisiae	Mutation(s): 0
UniProt
Find proteins for P53540 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53540  Go to UniProtKB:  P53540

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TUBULIN GAMMA CHAIN	C, D	473	Saccharomyces cerevisiae	Mutation(s): 2
UniProt
Find proteins for P53378 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53378  Go to UniProtKB:  P53378

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SPINDLE POLE BODY COMPONENT 110	E, F	44	Saccharomyces cerevisiae	Mutation(s): 0

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-10-29 
• Released Date: 2016-01-13 
Deposition Author(s): Greenberg, C.H., Kollman, J., Zelter, A., Johnson, R., MacCoss, M.J., Davis, T.N., Agard, D.A., Sali, A.

Revision History  

• 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