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- PDB-8fw5: Chimeric HsGATOR1-SpGtr-SpLam complex -

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Basic information

Entry
Database: PDB / ID: 8fw5
TitleChimeric HsGATOR1-SpGtr-SpLam complex
Components
  • (GATOR complex protein ...) x 3
  • (GTP-binding protein ...G protein) x 2
  • (Schizosaccharomyces pombe ...) x 4
KeywordsSIGNALING PROTEIN / mTOR complex 1 (mTORC1) / Rag GTPase / Gtr GTPase / LAMTOR / GATOR1 / nutrient sensing
Function / homology
Function and homology information


GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / negative regulation of TOR signaling / cardiac muscle tissue development / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / roof of mouth development ...GATOR1 complex / aorta morphogenesis / TORC1 signaling / Amino acids regulate mTORC1 / negative regulation of TOR signaling / cardiac muscle tissue development / vacuolar membrane / ventricular septum development / negative regulation of kinase activity / roof of mouth development / positive regulation of autophagy / negative regulation of TORC1 signaling / cellular response to amino acid starvation / GTPase activator activity / small GTPase binding / lysosome / intracellular signal transduction / lysosomal membrane / protein-containing complex binding / perinuclear region of cytoplasm / cytosol
Similarity search - Function
: / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein C-terminal region / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) ...: / Nitrogen permease regulator 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein, C-terminal / Nitrogen Permease regulator of amino acid transport activity 3 / Nitrogen permease regulator 2 / Vacuolar membrane-associated protein Iml1 / DEPDC5 protein C-terminal region / Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) / DEP domain profile. / Domain found in Dishevelled, Egl-10, and Pleckstrin / DEP domain / Winged helix DNA-binding domain superfamily / Winged helix-like DNA-binding domain superfamily
Similarity search - Domain/homology
ALUMINUM FLUORIDE / GUANOSINE-5'-DIPHOSPHATE / GATOR1 complex protein DEPDC5 / GATOR1 complex protein NPRL3 / GATOR1 complex protein NPRL2
Similarity search - Component
Biological speciesHomo sapiens (human)
Escherichia coli (E. coli)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.08 Å
AuthorsTettoni, S.D. / Egri, S.B. / Doxsey, D.D. / Ouch, C. / Chang, J. / Song, K. / Xu, C. / Shen, K.
Funding support United States, 2items
OrganizationGrant numberCountry
American Heart Association United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Structure / Year: 2023
Title: Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing.
Authors: Steven D Tettoni / Shawn B Egri / Dylan D Doxsey / Kristen Veinotte / Christna Ouch / Jeng-Yih Chang / Kangkang Song / Chen Xu / Kuang Shen /
Abstract: mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream ...mTORC1 is a protein kinase complex that controls cellular growth in response to nutrient availability. Amino acid signals are transmitted toward mTORC1 via the Rag/Gtr GTPases and their upstream regulators. An important regulator is LAMTOR, which localizes Rag/Gtr on the lysosomal/vacuole membrane. In human cells, LAMTOR consists of five subunits, but in yeast, only three or four. Currently, it is not known how variation of the subunit stoichiometry may affect its structural organization and biochemical properties. Here, we report a 3.1 Å-resolution structural model of the Gtr-Lam complex in Schizosaccharomyces pombe. We found that SpGtr shares conserved architecture as HsRag, but the intersubunit communication that coordinates nucleotide loading on the two subunits differs. In contrast, SpLam contains distinctive structural features, but its GTP-specific GEF activity toward SpGtr is evolutionarily conserved. Our results revealed unique evolutionary paths of the protein components of the mTORC1 pathway.
History
DepositionJan 20, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 26, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GATOR complex protein DEPDC5
B: GATOR complex protein NPRL2
C: GATOR complex protein NPRL3
D: GTP-binding protein Gtr1
E: GTP-binding protein Gtr2
F: Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog
G: Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog
H: Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog
I: Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)451,14613
Polymers450,1529
Non-polymers9954
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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GATOR complex protein ... , 3 types, 3 molecules ABC

#1: Protein GATOR complex protein DEPDC5 / DEP domain-containing protein 5


Mass: 181325.828 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DEPDC5, KIAA0645 / Production host: Homo sapiens (human) / References: UniProt: O75140
#2: Protein GATOR complex protein NPRL2 / Gene 21 protein / G21 protein / Nitrogen permease regulator 2-like protein / NPR2-like protein / ...Gene 21 protein / G21 protein / Nitrogen permease regulator 2-like protein / NPR2-like protein / Tumor suppressor candidate 4


Mass: 45799.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPRL2, TUSC4 / Production host: Homo sapiens (human) / References: UniProt: Q8WTW4
#3: Protein GATOR complex protein NPRL3 / -14 gene protein / Alpha-globin regulatory element-containing gene protein / Nitrogen permease ...-14 gene protein / Alpha-globin regulatory element-containing gene protein / Nitrogen permease regulator 3-like protein / Protein CGTHBA


Mass: 65769.000 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NPRL3, C16orf35, CGTHBA, MARE / Production host: Homo sapiens (human) / References: UniProt: Q12980

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GTP-binding protein ... , 2 types, 2 molecules DE

#4: Protein GTP-binding protein Gtr1


Mass: 36500.449 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#5: Protein GTP-binding protein Gtr2


Mass: 35547.559 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Schizosaccharomyces pombe ... , 4 types, 4 molecules FGHI

#6: Protein Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog


Mass: 43686.832 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#7: Protein Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog


Mass: 19830.908 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#8: Protein Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog


Mass: 12707.468 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)
#9: Protein Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog


Mass: 8984.198 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Production host: Escherichia coli (E. coli)

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Non-polymers , 3 types, 4 molecules

#10: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: GDP, energy-carrying molecule*YM
#11: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#12: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Chimeric HsGATOR1-SpGtr-SpLam complex / Type: COMPLEX / Entity ID: #1-#9 / Source: MULTIPLE SOURCES
Molecular weightValue: 0.42 MDa / Experimental value: YES
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50.7 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 659887 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00423327
ELECTRON MICROSCOPYf_angle_d0.831612
ELECTRON MICROSCOPYf_dihedral_angle_d6.2153078
ELECTRON MICROSCOPYf_chiral_restr0.0513601
ELECTRON MICROSCOPYf_plane_restr0.0064019

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