6JM5 | pdb_00006jm5

Crystal structure of TBC1D23 C terminal domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 
    0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work: 
    0.157 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6JM5

This is version 1.3 of the entry. See complete history

Literature

Structural and functional studies of TBC1D23 C-terminal domain provide a link between endosomal trafficking and PCH.

Huang, W.Liu, Z.Yang, F.Zhou, H.Yong, X.Yang, X.Zhou, Y.Xue, L.Zhang, Y.Liu, D.Meng, W.Zhang, W.Zhang, X.Shen, X.Sun, Q.Li, L.Ma, C.Wei, Y.Billadeau, D.D.Mo, X.Jia, D.

(2019) Proc Natl Acad Sci U S A 116: 22598-22608

  • DOI: https://doi.org/10.1073/pnas.1909316116
  • Primary Citation Related Structures: 
    6JM5

  • PubMed Abstract: 

    Pontocerebellar hypoplasia (PCH) is a group of neurological disorders that affect the development of the brain, in particular, the pons and cerebellum. Homozygous mutations of TBC1D23 have been found recently to lead to PCH; however, the underlying molecular mechanisms remain unclear. Here, we show that the crystal structure of the TBC1D23 C-terminal domain adopts a Pleckstrin homology domain fold and selectively binds to phosphoinositides, in particular, PtdIns(4)P, through one surface while binding FAM21 via the opposite surface. Mutation of key residues of TBC1D23 or FAM21 selectively disrupts the endosomal vesicular trafficking toward the Trans-Golgi Network. Finally, using the zebrafish model, we show that PCH patient-derived mutants, impacting either phosphoinositide binding or FAM21 binding, lead to abnormal neuronal growth and brain development. Taken together, our data provide a molecular basis for the interaction between TBC1D23 and FAM21, and suggest a plausible role for PtdIns(4)P in the TBC1D23-mediating endosome-to-TGN trafficking pathway. Defects in this trafficking pathway are, at least partially, responsible for the pathogenesis of certain types of PCH.


  • Organizational Affiliation
    • Key Laboratory of Birth Defects and Related Diseases of Women and Children, Department of Paediatrics, West China Second University Hospital, State Key Laboratory of Biotherapy and Collaborative Innovation Center of Biotherapy, Sichuan University, Chengdu 610041, China.

Macromolecule Content 

  • Total Structure Weight: 27.81 kDa 
  • Atom Count: 2,210 
  • Modeled Residue Count: 244 
  • Deposited Residue Count: 246 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
TBC1 domain family member 23
A, B
123Homo sapiensMutation(s): 0 
Gene Names: TBC1D23NS4ATP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUY8 (Homo sapiens)
Explore Q9NUY8 
Go to UniProtKB:  Q9NUY8
PHAROS:  Q9NUY8
GTEx:  ENSG00000036054 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUY8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA

Query on NA



Download:Ideal Coordinates CCD File
C [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free:  0.207 (Depositor), 0.207 (DCC) 
  • R-Value Work:  0.157 (Depositor), 0.162 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 130.822α = 90
b = 48.95β = 109.64
c = 47.439γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
AutoSolphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-10-16
    Type: Initial release
  • Version 1.1: 2019-10-30
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Database references, Structure summary
  • Version 1.3: 2024-03-27
    Changes: Data collection, Database references, Derived calculations