5GTU

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

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • 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 (NIH/NIGMS), Howard Hughes Medical Institute, CNSF, Welch Foundation

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1038/ncomms13305
  • Primary Citation of Related Structures:  
    5GTU

  • 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vacuolar protein sorting-associated protein 29186Homo sapiensMutation(s): 0 
Gene Names: VPS29DC15DC7MDS007
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBQ0 (Homo sapiens)
Explore Q9UBQ0 
Go to UniProtKB:  Q9UBQ0
PHAROS:  Q9UBQ0
GTEx:  ENSG00000111237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UBQ0
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
TBC1 domain family member 527Homo sapiensMutation(s): 0 
Gene Names: TBC1D5KIAA0210
UniProt & NIH Common Fund Data Resources
Find proteins for Q92609 (Homo sapiens)
Explore Q92609 
Go to UniProtKB:  Q92609
PHAROS:  Q92609
GTEx:  ENSG00000131374 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92609
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.186 
  • R-Value Work: 0.139 
  • R-Value Observed: 0.141 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.881α = 90
b = 63.832β = 90
c = 78.01γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01-GM056322
Howard Hughes Medical InstituteUnited States--
CNSFChinaJunior One Thousand Talents program
Welch FoundationUnited StatesI-1544

Revision History  (Full details and data files)

  • Version 1.0: 2016-12-07
    Type: Initial release
  • Version 1.1: 2017-10-18
    Changes: Author supporting evidence
  • Version 1.2: 2022-03-23
    Changes: Author supporting evidence, Database references
  • Version 1.3: 2023-11-08
    Changes: Data collection, Refinement description