5FM1

Structure of gamma-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure

Summary for 5FM1

• Entry DOI: 10.2210/pdb5fm1/pdb
• Related: 5FLZ
• EMDB information: 1731
• Descriptor: SPINDLE POLE BODY COMPONENT SPC97, SPINDLE POLE BODY COMPONENT SPC98, TUBULIN GAMMA CHAIN, ... (4 entities in total)
• Functional Keywords: cell cycle, microtubule, nucleation, tubulin, filament
• Biological source: SACCHAROMYCES CEREVISIAE (BAKER'S YEAST); More
• Cellular location: Nucleus: P38863 P53540; Cytoplasm, cytoskeleton, microtubule organizing center, spindle pole body: P53378
• Total number of polymer chains: 6
• Total formula weight: 308144.44

Authors

Greenberg, C.H.,Kollman, J.,Zelter, A.,Johnson, R.,MacCoss, M.J.,Davis, T.N.,Agard, D.A.,Sali, A. (deposition date: 2015-10-30, release date: 2016-02-03, Last modification date: 2024-05-08)

Primary citation

Greenberg, C.H.,Kollman, J.,Zelter, A.,Johnson, R.,Maccoss, M.J.,Davis, T.N.,Agard, D.A.,Sali, A.
Structure of Gamma-Tubulin Small Complex Based on a Cryo-Em Map, Chemical Cross-Links, and a Remotely Related Structure.
J.Struct.Biol., 194:303-, 2016

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.

PubMed: 26968363
DOI: 10.1016/J.JSB.2016.03.006

Experimental method

ELECTRON MICROSCOPY (8 Å)