7CC7

Tetratricopeptide repeat (TPR) domain of protein tyrosine phosphatase-interacting protein 51 (PTPIP51)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 

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Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history


Literature

Phospholipid transfer function of PTPIP51 at mitochondria-associated ER membranes.

Yeo, H.K.Park, T.H.Kim, H.Y.Jang, H.Lee, J.Hwang, G.S.Ryu, S.E.Park, S.H.Song, H.K.Ban, H.S.Yoon, H.J.Lee, B.I.

(2021) EMBO Rep 22: e51323-e51323

  • DOI: https://doi.org/10.15252/embr.202051323
  • Primary Citation of Related Structures:  
    7CC7

  • PubMed Abstract: 

    In eukaryotic cells, mitochondria are closely tethered to the endoplasmic reticulum (ER) at sites called mitochondria-associated ER membranes (MAMs). Ca 2+ ion and phospholipid transfer occurs at MAMs to support diverse cellular functions. Unlike those in yeast, the protein complexes involved in phospholipid transfer at MAMs in humans have not been identified. Here, we determine the crystal structure of the tetratricopeptide repeat domain of PTPIP51 (PTPIP51_TPR), a mitochondrial protein that interacts with the ER-anchored VAPB protein at MAMs. The structure of PTPIP51_TPR shows an archetypal TPR fold, and an electron density map corresponding to an unidentified lipid-like molecule probably derived from the protein expression host is found in the structure. We reveal functions of PTPIP51 in phospholipid binding/transfer, particularly of phosphatidic acid, in vitro. Depletion of PTPIP51 in cells reduces the mitochondrial cardiolipin level. Additionally, we confirm that the PTPIP51-VAPB interaction is mediated by the FFAT-like motif of PTPIP51 and the MSP domain of VAPB. Our findings suggest that PTPIP51 is a phospholipid transfer protein with a MAM-tethering function.


  • Organizational Affiliation

    Research Institute, National Cancer Center, Goyang-si, Korea.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulator of microtubule dynamics protein 3235Homo sapiensMutation(s): 0 
Gene Names: RMDN3FAM82A2FAM82CPTPIP51hucep-10UNQ3122/PRO10274
UniProt & NIH Common Fund Data Resources
Find proteins for Q96TC7 (Homo sapiens)
Explore Q96TC7 
Go to UniProtKB:  Q96TC7
PHAROS:  Q96TC7
GTEx:  ENSG00000137824 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96TC7
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.193 
  • Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 80.025α = 90
b = 80.025β = 90
c = 202.893γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Research Foundation (NRF, Korea)Korea, Republic Of2019R1A2C1002545

Revision History  (Full details and data files)

  • Version 1.0: 2021-01-20
    Type: Initial release
  • Version 1.1: 2021-03-10
    Changes: Source and taxonomy
  • Version 1.2: 2021-05-12
    Changes: Database references
  • Version 1.3: 2021-05-19
    Changes: Database references
  • Version 1.4: 2021-06-23
    Changes: Database references
  • Version 1.5: 2024-03-27
    Changes: Data collection, Database references