8FW5 | pdb_00008fw5

Chimeric HsGATOR1-SpGtr-SpLam complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Structure of the Schizosaccharomyces pombe Gtr-Lam complex reveals evolutionary divergence of mTORC1-dependent amino acid sensing.

Tettoni, S.D.Egri, S.B.Doxsey, D.D.Veinotte, K.Ouch, C.Chang, J.Y.Song, K.Xu, C.Shen, K.

(2023) Structure 31: 1065-1076.e5

  • DOI: https://doi.org/10.1016/j.str.2023.06.012
  • Primary Citation Related Structures: 
    8FW5

  • PubMed 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 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.


  • Organizational Affiliation
    • Program in Molecular Medicine, University of Massachusetts Chan Medical School, 373 Plantation Street, Worcester, MA 01605, USA.

Macromolecule Content 

  • Total Structure Weight: 451.15 kDa 
  • Atom Count: 22,853 
  • Modeled Residue Count: 2,832 
  • Deposited Residue Count: 3,985 
  • Unique protein chains: 9

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
GATOR complex protein DEPDC51,603Homo sapiensMutation(s): 1 
Gene Names: DEPDC5KIAA0645
UniProt & NIH Common Fund Data Resources
Find proteins for O75140 (Homo sapiens)
Explore O75140 
Go to UniProtKB:  O75140
PHAROS:  O75140
GTEx:  ENSG00000100150 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75140
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
GATOR complex protein NPRL2401Homo sapiensMutation(s): 0 
Gene Names: NPRL2TUSC4
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WTW4 (Homo sapiens)
Explore Q8WTW4 
Go to UniProtKB:  Q8WTW4
PHAROS:  Q8WTW4
GTEx:  ENSG00000114388 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8WTW4
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
GATOR complex protein NPRL3590Homo sapiensMutation(s): 0 
Gene Names: NPRL3C16orf35CGTHBAMARE
UniProt & NIH Common Fund Data Resources
Find proteins for Q12980 (Homo sapiens)
Explore Q12980 
Go to UniProtKB:  Q12980
PHAROS:  Q12980
GTEx:  ENSG00000103148 
Entity Groups
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UniProt GroupQ12980
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding protein Gtr1321Escherichia coliMutation(s): 0 
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
GTP-binding protein Gtr2314Escherichia coliMutation(s): 0 
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Entity ID: 6
MoleculeChains  Sequence LengthOrganismDetailsImage
Schizosaccharomyces pombe LAM1, Human LAMTOR1 ortholog377Escherichia coliMutation(s): 0 
EC: 2.5.1.18
UniProt
Find proteins for P08515 (Schistosoma japonicum)
Explore P08515 
Go to UniProtKB:  P08515
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UniProt GroupP08515
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Reference Sequence
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Entity ID: 7
MoleculeChains  Sequence LengthOrganismDetailsImage
Schizosaccharomyces pombe LAM2, Human LAMTOR2 ortholog181Escherichia coliMutation(s): 0 
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Entity ID: 8
MoleculeChains  Sequence LengthOrganismDetailsImage
Schizosaccharomyces pombe LAM3, Human LAMTOR3 ortholog117Escherichia coliMutation(s): 0 
Find similar proteins by:|  3D Structure
Entity ID: 9
MoleculeChains  Sequence LengthOrganismDetailsImage
Schizosaccharomyces pombe LAM4, Human LAMTOR5 ortholog81Escherichia coliMutation(s): 0 

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.08 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
American Heart AssociationUnited States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2023-07-26
    Type: Initial release
  • Version 1.1: 2023-09-20
    Changes: Data collection, Database references
  • Version 1.2: 2025-05-14
    Changes: Data collection, Structure summary