6B9X | pdb_00006b9x

Crystal structure of Ragulator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free: 
    0.237 (Depositor), 0.246 (DCC) 
  • R-Value Work: 
    0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6B9X

This is version 1.4 of the entry. See complete history

Literature

Hybrid Structure of the RagA/C-Ragulator mTORC1 Activation Complex.

Su, M.Y.Morris, K.L.Kim, D.J.Fu, Y.Lawrence, R.Stjepanovic, G.Zoncu, R.Hurley, J.H.

(2017) Mol Cell 68: 835-846.e3

  • DOI: https://doi.org/10.1016/j.molcel.2017.10.016
  • Primary Citation Related Structures: 
    6B9X

  • PubMed Abstract: 

    The lysosomal membrane is the locus for sensing cellular nutrient levels, which are transduced to mTORC1 via the Rag GTPases and the Ragulator complex. The crystal structure of the five-subunit human Ragulator at 1.4 Å resolution was determined. Lamtor1 wraps around the other four subunits to stabilize the assembly. The Lamtor2:Lamtor3 dimer stacks upon Lamtor4:Lamtor5 to create a platform for Rag binding. Hydrogen-deuterium exchange was used to map the Rag binding site to the outer face of the Lamtor2:Lamtor3 dimer and to the N-terminal intrinsically disordered region of Lamtor1. EM was used to reconstruct the assembly of the full-length RagA GTP :RagC GDP dimer bound to Ragulator at 16 Å resolution, revealing that the G-domains of the Rags project away from the Ragulator core. The combined structural model shows how Ragulator functions as a platform for the presentation of active Rags for mTORC1 recruitment, and might suggest an unconventional mechanism for Rag GEF activity.


  • Organizational Affiliation
    • Department of Molecular and Cell Biology and California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA.

Macromolecule Content 

  • Total Structure Weight: 73.92 kDa 
  • Atom Count: 3,997 
  • Modeled Residue Count: 488 
  • Deposited Residue Count: 683 
  • Unique protein chains: 5

Macromolecules

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Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR1161Homo sapiensMutation(s): 0 
Gene Names: LAMTOR1C11orf59PDROPP7157
UniProt & NIH Common Fund Data Resources
Find proteins for Q6IAA8 (Homo sapiens)
Explore Q6IAA8 
Go to UniProtKB:  Q6IAA8
PHAROS:  Q6IAA8
GTEx:  ENSG00000149357 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ6IAA8
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Reference Sequence
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Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR2126Homo sapiensMutation(s): 0 
Gene Names: LAMTOR2MAPBPIPROBLD3HSPC003
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y2Q5 (Homo sapiens)
Explore Q9Y2Q5 
Go to UniProtKB:  Q9Y2Q5
PHAROS:  Q9Y2Q5
GTEx:  ENSG00000116586 
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UniProt GroupQ9Y2Q5
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Reference Sequence
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Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR3124Homo sapiensMutation(s): 0 
Gene Names: LAMTOR3MAP2K1IP1MAPKSP1PRO2783
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UHA4 (Homo sapiens)
Explore Q9UHA4 
Go to UniProtKB:  Q9UHA4
PHAROS:  Q9UHA4
GTEx:  ENSG00000109270 
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UniProt GroupQ9UHA4
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Reference Sequence
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Entity ID: 4
MoleculeChains  Sequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR499Homo sapiensMutation(s): 0 
Gene Names: LAMTOR4C7orf59
UniProt & NIH Common Fund Data Resources
Find proteins for Q0VGL1 (Homo sapiens)
Explore Q0VGL1 
Go to UniProtKB:  Q0VGL1
PHAROS:  Q0VGL1
GTEx:  ENSG00000188186 
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UniProt GroupQ0VGL1
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Reference Sequence
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Entity ID: 5
MoleculeChains  Sequence LengthOrganismDetailsImage
Hepatitis B virus x interacting protein173Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPhCG_40252
UniProt & NIH Common Fund Data Resources
Find proteins for O43504 (Homo sapiens)
Explore O43504 
Go to UniProtKB:  O43504
PHAROS:  O43504
GTEx:  ENSG00000134248 
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UniProt GroupO43504
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.42 Å
  • R-Value Free:  0.237 (Depositor), 0.246 (DCC) 
  • R-Value Work:  0.212 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.705α = 90
b = 168.705β = 90
c = 52.325γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PHASERphasing
Cootmodel building
XDSdata reduction
XDSdata scaling

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/Office of the DirectorUnited States1DP2CA195761-01

Revision History  (Full details and data files)

  • Version 1.0: 2017-11-08
    Type: Initial release
  • Version 1.1: 2017-11-22
    Changes: Database references
  • Version 1.2: 2017-12-20
    Changes: Database references
  • Version 1.3: 2022-03-16
    Changes: Author supporting evidence, Database references
  • Version 1.4: 2023-10-04
    Changes: Data collection, Refinement description