5GTU

Structural and mechanistic insights into regulation of the retromer coat by TBC1d5

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli

  • Deposited: 2016-08-23 Released: 2016-12-07 
  • Deposition Author(s): Jia, D., Rosen, M.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; Howard Hughes Medical Institute; CNSF; Welch Foundation 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and mechanistic insights into regulation of the retromer coat by TBC1d5

Jia, D.Zhang, J.S.Li, F.Wang, J.Deng, Z.White, M.A.Osborne, D.G.Phillips-Krawczak, C.Gomez, T.S.Li, H.Singla, A.Burstein, E.Billadeau, D.D.Rosen, M.K.

(2016) Nat Commun 7: 13305-13305

  • DOI: 10.1038/ncomms13305

  • PubMed Abstract: 
  • Retromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Her ...

    Retromer is a membrane coat complex that is recruited to endosomes by the small GTPase Rab7 and sorting nexin 3. The timing of this interaction and consequent endosomal dynamics are thought to be regulated by the guanine nucleotide cycle of Rab7. Here we demonstrate that TBC1d5, a GTPase-activating protein (GAP) for Rab7, is a high-affinity ligand of the retromer cargo selective complex VPS26/VPS29/VPS35. The crystal structure of the TBC1d5 GAP domain bound to VPS29 and complementary biochemical and cellular data show that a loop from TBC1d5 binds to a conserved hydrophobic pocket on VPS29 opposite the VPS29-VPS35 interface. Additional data suggest that a distinct loop of the GAP domain may contact VPS35. Loss of TBC1d5 causes defective retromer-dependent trafficking of receptors. Our findings illustrate how retromer recruits a GAP, which is likely to be involved in the timing of Rab7 inactivation leading to membrane uncoating, with important consequences for receptor trafficking.


    Organizational Affiliation

    Key Laboratory of Birth Defects and Related Diseases of Women and Children (Ministry of Education), Department of Paediatrics, West China Second University Hospital and State Key Laboratory of Biotherapy, Sichuan University, Chengdu 610041, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vacuolar protein sorting-associated protein 29
A
186Homo sapiensMutation(s): 0 
Gene Names: VPS29
Find proteins for Q9UBQ0 (Homo sapiens)
Go to Gene View: VPS29
Go to UniProtKB:  Q9UBQ0
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TBC1 domain family member 5
B
27Homo sapiensMutation(s): 0 
Gene Names: TBC1D5 (KIAA0210)
Find proteins for Q92609 (Homo sapiens)
Go to Gene View: TBC1D5
Go to UniProtKB:  Q92609
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 43.881α = 90.00
b = 63.832β = 90.00
c = 78.010γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-3000data reduction
HKL-3000data scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2016-08-23 
  • Released Date: 2016-12-07 
  • Deposition Author(s): Jia, D., Rosen, M.

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR01-GM056322
Howard Hughes Medical InstituteUnited States--
CNSFChinaJunior One Thousand Talents program
Welch FoundationUnited StatesI-1544

Revision History 

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-10-18
    Type: Author supporting evidence