6OAZ

Apo Structure of WT Lipoprotein Lipase in Complex with GPIHBP1 Mutant N78D N82D produced in HEK293-F cells


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 

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This is version 1.4 of the entry. See complete history


Literature

Structure of lipoprotein lipase in complex with GPIHBP1.

Arora, R.Nimonkar, A.V.Baird, D.Wang, C.Chiu, C.H.Horton, P.A.Hanrahan, S.Cubbon, R.Weldon, S.Tschantz, W.R.Mueller, S.Brunner, R.Lehr, P.Meier, P.Ottl, J.Voznesensky, A.Pandey, P.Smith, T.M.Stojanovic, A.Flyer, A.Benson, T.E.Romanowski, M.J.Trauger, J.W.

(2019) Proc Natl Acad Sci U S A 116: 10360-10365

  • DOI: https://doi.org/10.1073/pnas.1820171116
  • Primary Citation of Related Structures:  
    6OAU, 6OAZ, 6OB0

  • PubMed Abstract: 

    Lipoprotein lipase (LPL) plays a central role in triglyceride (TG) metabolism. By catalyzing the hydrolysis of TGs present in TG-rich lipoproteins (TRLs), LPL facilitates TG utilization and regulates circulating TG and TRL concentrations. Until very recently, structural information for LPL was limited to homology models, presumably due to the propensity of LPL to unfold and aggregate. By coexpressing LPL with a soluble variant of its accessory protein glycosylphosphatidylinositol-anchored high-density lipoprotein binding protein 1 (GPIHBP1) and with its chaperone protein lipase maturation factor 1 (LMF1), we obtained a stable and homogenous LPL/GPIHBP1 complex that was suitable for structure determination. We report here X-ray crystal structures of human LPL in complex with human GPIHBP1 at 2.5-3.0 Å resolution, including a structure with a novel inhibitor bound to LPL. Binding of the inhibitor resulted in ordering of the LPL lid and lipid-binding regions and thus enabled determination of the first crystal structure of LPL that includes these important regions of the protein. It was assumed for many years that LPL was only active as a homodimer. The structures and additional biochemical data reported here are consistent with a new report that LPL, in complex with GPIHBP1, can be active as a monomeric 1:1 complex. The crystal structures illuminate the structural basis for LPL-mediated TRL lipolysis as well as LPL stabilization and transport by GPIHBP1.


  • Organizational Affiliation

    Chemical Biology and Therapeutics, 4002 Basel, Switzerland.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Lipoprotein lipase
A, B, C, D
448Homo sapiensMutation(s): 0 
Gene Names: GPIHBP1HBP1
EC: 3.1.1.34
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for P06858 (Homo sapiens)
Explore P06858 
Go to UniProtKB:  P06858
PHAROS:  P06858
GTEx:  ENSG00000175445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06858
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1
E, F, G, H
131Homo sapiensMutation(s): 2 
Gene Names: GPIHBP1HBP1
Membrane Entity: Yes 
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV16 (Homo sapiens)
Explore Q8IV16 
Go to UniProtKB:  Q8IV16
PHAROS:  Q8IV16
GTEx:  ENSG00000277494 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV16
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
I [auth A]
J [auth A]
O [auth B]
AA [auth D],
BA [auth D],
I [auth A],
J [auth A],
O [auth B],
P [auth B],
U [auth C],
V [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
CA [auth D]
DA [auth D]
K [auth A]
L [auth A]
Q [auth B]
CA [auth D],
DA [auth D],
K [auth A],
L [auth A],
Q [auth B],
R [auth B],
W [auth C],
X [auth C]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth D]
M [auth A]
N [auth A]
S [auth B]
EA [auth D],
FA [auth D],
M [auth A],
N [auth A],
S [auth B],
T [auth B],
Y [auth C],
Z [auth C]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.04 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.203 
  • R-Value Observed: 0.205 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 157α = 90
b = 191.94β = 90
c = 96.06γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-05-08
    Type: Initial release
  • Version 1.1: 2019-05-22
    Changes: Data collection, Database references
  • Version 1.2: 2019-06-05
    Changes: Data collection, Database references
  • Version 1.3: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.4: 2023-10-11
    Changes: Data collection, Database references, Refinement description, Structure summary