5Y3A

Crystal structure of Ragulator complex (p18 49-161)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis for Ragulator functioning as a scaffold in membrane-anchoring of Rag GTPases and mTORC1.

Zhang, T.Wang, R.Wang, Z.Wang, X.Wang, F.Ding, J.

(2017) Nat Commun 8: 1394-1394

  • DOI: https://doi.org/10.1038/s41467-017-01567-4
  • Primary Citation of Related Structures:  
    5Y38, 5Y39, 5Y3A

  • PubMed Abstract: 

    Amino acid-dependent activation of the mechanistic target of rapamycin complex 1 (mTORC1) is mediated by Rag GTPases, which are recruited to the lysosome by the Ragulator complex consisting of p18, MP1, p14, HBXIP and C7orf59; however, the molecular mechanism is elusive. Here, we report the crystal structure of Ragulator, in which p18 wraps around the MP1-p14 and C7orf59-HBXIP heterodimers and the interactions of p18 with MP1, C7orf59, and HBXIP are essential for the assembly of Ragulator. There are two binding sites for the Roadblock domains of Rag GTPases: helix α1 of p18 and the two helices side of MP1-p14. The interaction of Ragulator with Rag GTPases is required for their cellular co-localization and can be competitively inhibited by C17orf59. Collectively, our data indicate that Ragulator functions as a scaffold to recruit Rag GTPases to lysosomal membrane in mTORC1 signaling.


  • Organizational Affiliation

    State Key Laboratory of Molecular Biology, National Center for Protein Science Shanghai, Shanghai Science Research Center, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, 320 Yue-Yang Road, Shanghai, 200031, China.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1
A, F
112Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
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PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
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UniProt GroupQ6IAA8
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2
B, G
127Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
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Find proteins for Q9Y2Q5 (Homo sapiens)
Explore Q9Y2Q5 
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PHAROS:  Q9Y2Q5
GTEx:  ENSG00000116586 
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UniProt GroupQ9Y2Q5
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3
C, H
124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
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PHAROS:  Q9UHA4
GTEx:  ENSG00000109270 
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UniProt GroupQ9UHA4
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR4
D, I
101Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
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Find proteins for Q0VGL1 (Homo sapiens)
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PHAROS:  Q0VGL1
GTEx:  ENSG00000188186 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5
E, J
93Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPXIP
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Find proteins for O43504 (Homo sapiens)
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PHAROS:  O43504
GTEx:  ENSG00000134248 
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.288 
  • R-Value Work: 0.246 
  • R-Value Observed: 0.248 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.341α = 90
b = 89.626β = 90
c = 232.173γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data scaling
PDB_EXTRACTdata extraction
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-27
    Type: Initial release
  • Version 1.1: 2023-11-22
    Changes: Data collection, Database references, Refinement description