5VOK

Crystal structure of the C7orf59-HBXIP dimer


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.285 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

C7orf59/Lamtor4 phosphorylation and structural flexibility modulate Ragulator assembly.

Rasheed, N.Lima, T.B.Mercaldi, G.F.Nascimento, A.F.Z.Silva, A.L.S.Righetto, G.L.Bar-Peled, L.Shen, K.Sabatini Shen, D.M.Gozzo, F.C.Aparicio, R.Smetana, J.H.C.

(2019) FEBS Open Bio 

  • DOI: 10.1002/2211-5463.12700
  • Primary Citation of Related Structures:  
    5VOK

  • PubMed Abstract: 
  • Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X-interacting protein (HBXIP; LAMTOR 1-5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP-C7orf59 dimer (LAMTOR 4/5) at 2 ...

    Ragulator is a pentamer composed of p18, MP1, p14, C7orf59, and hepatitis B virus X-interacting protein (HBXIP; LAMTOR 1-5) which acts as a lysosomal scaffold of the Rag GTPases in the amino acid sensitive branch of TORC1 signaling. Here, we present the crystal structure of human HBXIP-C7orf59 dimer (LAMTOR 4/5) at 2.9 Å and identify a phosphorylation site on C7orf59 which modulates its interaction with p18. Additionally, we demonstrate the requirement of HBXIP-C7orf59 to stabilize p18 and allow further binding of MP1-p14. The structure of the dimer revealed an unfolded N terminus in C7orf59 (residues 1-15) which was shown to be essential for p18 binding. Full-length p18 does not interact stably with MP1-p14 in the absence of HBXIP-C7orf59, but deletion of p18 residues 108-161 rescues MP1-p14 binding. C7orf59 was phosphorylated by protein kinase A (PKA) in vitro and mutation of the conserved Ser67 residue to aspartate prevented phosphorylation and negatively affected the C7orf59 interaction with p18 both in cell culture and in vitro. C7orf59 Ser67 was phosphorylated in human embryonic kidney 293T cells. PKA activation with forskolin induced dissociation of p18 from C7orf59, which was prevented by the PKA inhibitor H-89. Our results highlight the essential role of HBXIP-C7orf59 dimer as a nucleator of pentameric Ragulator and support a sequential model of Ragulator assembly in which HBXIP-C7orf59 binds and stabilizes p18 which allows subsequent binding of MP1-p14.


    Organizational Affiliation

    Brazilian Biosciences National Laboratory (LNBio), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Ragulator complex protein LAMTOR5A, C, E, G91Homo 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 LAMTOR4B, D, F, H103Homo 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
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.89 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.280 
  • R-Value Observed: 0.285 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 180.884α = 90
b = 64.763β = 115.18
c = 79.231γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
DIALSdata reduction
Aimlessdata scaling
MrBUMPphasing

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Conselho Nacional de Desenvolvimento Cientifico e Tecnologico (CNPq-Brazil)Brazil190174/2012-9
Fundacao de Amparo a Pesquisa do Estado de Sao Paulo (FAPESP-Brazil)Brazil2014/12445-0

Revision History  (Full details and data files)

  • Version 1.0: 2018-05-23
    Type: Initial release
  • Version 1.1: 2019-07-31
    Changes: Data collection, Database references