6E7K

Structure of the lipoprotein lipase GPIHBP1 complex that mediates plasma triglyceride hydrolysis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 

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This is version 2.0 of the entry. See complete history


Literature

Structure of the lipoprotein lipase-GPIHBP1 complex that mediates plasma triglyceride hydrolysis.

Birrane, G.Beigneux, A.P.Dwyer, B.Strack-Logue, B.Kristensen, K.K.Francone, O.L.Fong, L.G.Mertens, H.D.T.Pan, C.Q.Ploug, M.Young, S.G.Meiyappan, M.

(2019) Proc Natl Acad Sci U S A 116: 1723-1732

  • DOI: 10.1073/pnas.1817984116
  • Primary Citation of Related Structures:  
    6E7K

  • PubMed Abstract: 
  • Lipoprotein lipase (LPL) is responsible for the intravascular processing of triglyceride-rich lipoproteins. The LPL within capillaries is bound to GPIHBP1, an endothelial cell protein with a three-fingered LU domain and an N-terminal intrinsically disordered acidic domain ...

    Lipoprotein lipase (LPL) is responsible for the intravascular processing of triglyceride-rich lipoproteins. The LPL within capillaries is bound to GPIHBP1, an endothelial cell protein with a three-fingered LU domain and an N-terminal intrinsically disordered acidic domain. Loss-of-function mutations in LPL or GPIHBP1 cause severe hypertriglyceridemia (chylomicronemia), but structures for LPL and GPIHBP1 have remained elusive. Inspired by our recent discovery that GPIHBP1's acidic domain preserves LPL structure and activity, we crystallized an LPL-GPIHBP1 complex and solved its structure. GPIHBP1's LU domain binds to LPL's C-terminal domain, largely by hydrophobic interactions. Analysis of electrostatic surfaces revealed that LPL contains a large basic patch spanning its N- and C-terminal domains. GPIHBP1's acidic domain was not defined in the electron density map but was positioned to interact with LPL's large basic patch, providing a likely explanation for how GPIHBP1 stabilizes LPL. The LPL-GPIHBP1 structure provides insights into mutations causing chylomicronemia.


    Organizational Affiliation

    Discovery Therapeutics, US Drug Discovery, Shire Pharmaceuticals, Cambridge, MA 02142; sgyoung@mednet.ucla.edu mmeiyappan@shire.com.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Lipoprotein lipaseA, B448Homo sapiensMutation(s): 1 
Gene Names: LPLLIPD
EC: 3.1.1.34 (PDB Primary Data), 3.1.1.32 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P06858 (Homo sapiens)
Explore P06858 
Go to UniProtKB:  P06858
PHAROS:  P06858
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06858
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glycosylphosphatidylinositol-anchored high density lipoprotein-binding protein 1C, D131Homo sapiensMutation(s): 0 
Gene Names: GPIHBP1HBP1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IV16 (Homo sapiens)
Explore Q8IV16 
Go to UniProtKB:  Q8IV16
PHAROS:  Q8IV16
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8IV16
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseE 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G15407YE
GlyCosmos:  G15407YE
GlyGen:  G15407YE
Entity ID: 4
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseF 4N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G32152BH
GlyCosmos:  G32152BH
GlyGen:  G32152BH
Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranoseG 3N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G21290RB
GlyCosmos:  G21290RB
GlyGen:  G21290RB
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
I [auth B],
K [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
H [auth A],
J [auth B]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.197 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 101.948α = 90
b = 153.206β = 90
c = 95.783γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2019-01-02
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-13
    Changes: Data collection, Database references
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary