8EC6 | pdb_00008ec6

Cryo-EM structure of the Glutaminase C core filament (fGAC)

• PDB DOI: https://doi.org/10.2210/pdb8EC6/pdb
• EM Map EMD-28013: EMDB EMDataResource

• Classification: HYDROLASE
• Organism(s): Mus musculus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2022-09-01 Released: 2023-09-20 
• Deposition Author(s): Ambrosio, A.L., Dias, S.M., Quesnay, J.E., Portugal, R.V., Cassago, A., van Heel, M.G., Islam, Z., Rodrigues, C.T.
• Funding Organization(s): Sao Paulo Research Foundation (FAPESP)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Molecular mechanism of glutaminase activation through filamentation and the role of filaments in mitophagy protection.

Adamoski, D., Dias, M.M., Quesnay, J.E.N., Yang, Z., Zagoriy, I., Steyer, A.M., Rodrigues, C.T., da Silva Bastos, A.C., da Silva, B.N., Costa, R.K.E., de Abreu, F.M.O., Islam, Z., Cassago, A., van Heel, M.G., Consonni, S.R., Mattei, S., Mahamid, J., Portugal, R.V., Ambrosio, A.L.B., Dias, S.M.G.

(2023) Nat Struct Mol Biol 30: 1902-1912

• PubMed: 37857822 
• DOI: https://doi.org/10.1038/s41594-023-01118-0
• Primary Citation Related Structures: 
  8EC6


• PubMed Abstract: 
  

  Glutaminase (GLS), which deaminates glutamine to form glutamate, is a mitochondrial tetrameric protein complex. Although inorganic phosphate (Pi) is known to promote GLS filamentation and activation, the molecular basis of this mechanism is unknown. Here we aimed to determine the molecular mechanism of Pi-induced mouse GLS filamentation and its impact on mitochondrial physiology. Single-particle cryogenic electron microscopy revealed an allosteric mechanism in which Pi binding at the tetramer interface and the activation loop is coupled to direct nucleophile activation at the active site. The active conformation is prone to enzyme filamentation. Notably, human GLS filaments form inside tubulated mitochondria following glutamine withdrawal, as shown by in situ cryo-electron tomography of cells thinned by cryo-focused ion beam milling. Mitochondria with GLS filaments exhibit increased protection from mitophagy. We reveal roles of filamentous GLS in mitochondrial morphology and recycling.

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Organizational Affiliation: 
• Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil.
Cancer Research UK Beatson Institute, Glasgow, UK.
Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil.
Institute of Chemistry, University of São Paulo, São Paulo, Brazil.
EMBL Imaging Centre, European Molecular Biology Laboratory, Heidelberg, Germany.
Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Biological Sciences Department, School of Science, Purdue University, Lafayette, IN, USA.
Division of Medical Oncology, Department of Internal Medicine, Washington University School of Medicine, St. Louis, MO, USA.
Graduate Program in Genetics and Molecular Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, USA.
Diabetes Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Qatar Foundation, Doha, Qatar.
Brazilian Nanotechnology National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil.
SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, USA.
Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas, Campinas, Brazil.
Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany.
Sao Carlos Institute of Physics, University of Sao Paulo, Sao Carlos, Brazil. [e-mail].
Brazilian Biosciences National Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, Brazil. [e-mail].

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 8-mer - A8 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 427.38 kDa 
• Atom Count: 19,133 
• Modeled Residue Count: 2,479 
• Deposited Residue Count: 3,832 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2 of Glutaminase kidney isoform, mitochondrial	A, B, C, D, E, F, G, H	479	Mus musculus	Mutation(s): 0  Gene Names: Gls, Gls1, Kiaa0838 EC: 3.5.1.2
UniProt & NIH Common Fund Data Resources
Find proteins for D3Z7P3 (Mus musculus) Explore D3Z7P3  Go to UniProtKB:  D3Z7P3
IMPC:  MGI:95752

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PO4 (Subject of Investigation/LOI)	I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.10 Å
• Aggregation State: FILAMENT 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2023-09-20 
Deposition Author(s): Ambrosio, A.L., Dias, S.M., Quesnay, J.E., Portugal, R.V., Cassago, A., van Heel, M.G., Islam, Z., Rodrigues, C.T.

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Funding Organization	Location	Grant Number
Sao Paulo Research Foundation (FAPESP)	Brazil	2017/11766-5

Revision History  

• Version 1.0: 2023-09-20
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Database references
• Version 1.2: 2023-11-01
  Changes: Database references
• Version 1.3: 2023-12-27
  Changes: Database references