6I3V

x-ray structure of the human mitochondrial PRELID1 in complex with TRIAP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Structural determinants of lipid specificity within Ups/PRELI lipid transfer proteins.

Miliara, X.Tatsuta, T.Berry, J.L.Rouse, S.L.Solak, K.Chorev, D.S.Wu, D.Robinson, C.V.Matthews, S.Langer, T.

(2019) Nat Commun 10: 1130-1130

  • DOI: 10.1038/s41467-019-09089-x
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Conserved lipid transfer proteins of the Ups/PRELI family regulate lipid accumulation in mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space. Here, we combine structural analysis, unbiased genetic approac ...

    Conserved lipid transfer proteins of the Ups/PRELI family regulate lipid accumulation in mitochondria by shuttling phospholipids in a lipid-specific manner across the intermembrane space. Here, we combine structural analysis, unbiased genetic approaches in yeast and molecular dynamics simulations to unravel determinants of lipid specificity within the conserved Ups/PRELI family. We present structures of human PRELID1-TRIAP1 and PRELID3b-TRIAP1 complexes, which exert lipid transfer activity for phosphatidic acid and phosphatidylserine, respectively. Reverse yeast genetic screens identify critical amino acid exchanges that broaden and swap their lipid specificities. We find that amino acids involved in head group recognition and the hydrophobicity of flexible loops regulate lipid entry into the binding cavity. Molecular dynamics simulations reveal different membrane orientations of PRELID1 and PRELID3b during the stepwise release of lipids. Our experiments thus define the structural determinants of lipid specificity and the dynamics of lipid interactions by Ups/PRELI proteins.


    Organizational Affiliation

    Department of Life Sciences, Imperial College London, Sir Ernst Chain Building, South Kensington, London, SW7 2AZ, UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PRELI domain-containing protein 1, mitochondrial
F, B
182Homo sapiensMutation(s): 0 
Gene Names: PRELID1 (PRELI)
Find proteins for Q9Y255 (Homo sapiens)
Go to Gene View: PRELID1
Go to UniProtKB:  Q9Y255
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
TP53-regulated inhibitor of apoptosis 1
A, C
69Homo sapiensMutation(s): 0 
Gene Names: TRIAP1 (15E1.1)
Find proteins for O43715 (Homo sapiens)
Go to Gene View: TRIAP1
Go to UniProtKB:  O43715
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MYR
Query on MYR

Download SDF File 
Download CCD File 
B, F
MYRISTIC ACID
C14 H28 O2
TUNFSRHWOTWDNC-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
B, C, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.205 
  • Space Group: P 63 2 2
Unit Cell:
Length (Å)Angle (°)
a = 127.312α = 90.00
b = 127.312β = 90.00
c = 177.390γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
United Kingdom--

Revision History 

  • Version 1.0: 2019-03-20
    Type: Initial release