6I3Y

Crystal structure of the human mitochondrial PRELID1K58V-TRIAP1 complex with PS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 

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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:  
    6I3Y, 6I3V, 6I4Y

  • 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 approaches in yeast and molecular dynamics simulations to unravel determinants of lipid specificity within the conserved Ups/PRELI family ...

    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

    Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), Center for Molecular Medicine (CMMC), University of Cologne, Joseph-Stelzmann-Str. 26, 50931, Cologne, Germany. Langer@age.mpg.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PRELI domain-containing protein 1, mitochondrialA [auth C], B [auth F]185Homo sapiensMutation(s): 1 
Gene Names: PRELID1PRELICGI-106SBBI12
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y255 (Homo sapiens)
Explore Q9Y255 
Go to UniProtKB:  Q9Y255
PHAROS:  Q9Y255
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
TP53-regulated inhibitor of apoptosis 1C [auth A], D [auth H]90Homo sapiensMutation(s): 0 
Gene Names: TRIAP115E1.1HSPC132
UniProt & NIH Common Fund Data Resources
Find proteins for O43715 (Homo sapiens)
Explore O43715 
Go to UniProtKB:  O43715
PHAROS:  O43715
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
P5S (Subject of Investigation/LOI)
Query on P5S

Download Ideal Coordinates CCD File 
F [auth C], G [auth F]O-[(R)-{[(2R)-2,3-bis(octadecanoyloxy)propyl]oxy}(hydroxy)phosphoryl]-L-serine
C42 H82 N O10 P
TZCPCKNHXULUIY-RGULYWFUSA-N
 Ligand Interaction
LMT (Subject of Investigation/LOI)
Query on LMT

Download Ideal Coordinates CCD File 
E [auth C]DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.244 
  • R-Value Observed: 0.247 
  • Space Group: P 63 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 126α = 90
b = 126β = 90
c = 178.32γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Medical Research Council (United Kingdom)United KingdomMR/M019403/1

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-20
    Type: Initial release
  • Version 1.1: 2019-04-10
    Changes: Data collection, Source and taxonomy