6I4Y

X-ray structure of the human mitochondrial PRELID3b-TRIAP1 complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 2.1 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: https://doi.org/10.1038/s41467-019-09089-x
  • Primary Citation of Related Structures:  
    6I3V, 6I3Y, 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. 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:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Maltose transport system, substrate-binding protein,TP53-regulated inhibitor of apoptosis 1446Escherichia coliHomo sapiens
This entity is chimeric
Mutation(s): 0 
Gene Names: malENCTC8450_00456NCTC9775_03059TRIAP115E1.1HSPC132
UniProt & NIH Common Fund Data Resources
Find proteins for P0AEX9 (Escherichia coli (strain K12))
Explore P0AEX9 
Go to UniProtKB:  P0AEX9
Find proteins for O43715 (Homo sapiens)
Explore O43715 
Go to UniProtKB:  O43715
PHAROS:  O43715
GTEx:  ENSG00000170855 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsO43715P0AEX9
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
PRELI domain containing protein 3B207Homo sapiensMutation(s): 0 
Gene Names: PRELID3BC20orf45SLMO2CGI-107
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y3B1 (Homo sapiens)
Explore Q9Y3B1 
Go to UniProtKB:  Q9Y3B1
PHAROS:  Q9Y3B1
GTEx:  ENSG00000101166 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y3B1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChains Length2D Diagram Glycosylation3D Interactions
alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G07411ON
GlyCosmos:  G07411ON
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download Ideal Coordinates CCD File 
D [auth B]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChains NameType/Class2D Diagram3D Interactions
PRD_900001
Query on PRD_900001
C
alpha-maltoseOligosaccharide / Nutrient
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.91 Å
  • R-Value Free: 0.296 
  • R-Value Work: 0.210 
  • R-Value Observed: 0.214 
  • Space Group: I 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.02α = 90
b = 133β = 90
c = 146.05γ = 90
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 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
  • Version 2.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary