5Y38

Crystal structure of C7orf59-HBXIP complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 

wwPDB Validation   3D Report Full Report


This is version 1.0 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: 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 ...

    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

    School of Life Science and Technology, ShanghaiTech University, 393 Hua-Xia Zhong Road, Shanghai, 201210, China. jpding@sibcb.ac.cn.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5A91Homo sapiensMutation(s): 0 
Gene Names: LAMTOR5HBXIPXIP
UniProt & NIH Common Fund Data Resources
Find proteins for O43504 (Homo sapiens)
Explore O43504 
Go to UniProtKB:  O43504
PHAROS:  O43504
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR4B109Homo 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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A], E [auth B]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.215 
  • R-Value Observed: 0.217 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.541α = 90
b = 58.541β = 90
c = 90.012γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
HKL-2000data scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

  • Deposited Date: 2017-07-28 
  • Released Date: 2017-12-06 
  • Deposition Author(s): Zhang, T., Ding, J.

Revision History  (Full details and data files)

  • Version 1.0: 2017-12-06
    Type: Initial release