3SO6

Crystal structure of the LDL receptor tail in complex with autosomal recessive hypercholesterolemia PTB domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Atomic structure of the autosomal recessive hypercholesterolemia phosphotyrosine-binding domain in complex with the LDL-receptor tail.

Dvir, H.Shah, M.Girardi, E.Guo, L.Farquhar, M.G.Zajonc, D.M.

(2012) Proc Natl Acad Sci U S A 109: 6916-6921

  • DOI: 10.1073/pnas.1114128109
  • Primary Citation of Related Structures:  
    3SO6

  • PubMed Abstract: 
  • Hypercholesterolemia, high serum cholesterol in the form of LDL, is a major risk factor for atherosclerosis. LDL is mostly degraded in the liver after its cellular internalization with the LDL receptor (LDLR). This clathrin-mediated endocytosis depends on the protein autosomal recessive hypercholesterolemia (ARH), which binds the LDLR cytoplasmic tail ...

    Hypercholesterolemia, high serum cholesterol in the form of LDL, is a major risk factor for atherosclerosis. LDL is mostly degraded in the liver after its cellular internalization with the LDL receptor (LDLR). This clathrin-mediated endocytosis depends on the protein autosomal recessive hypercholesterolemia (ARH), which binds the LDLR cytoplasmic tail. Mutations in either the LDLR tail or in ARH lead to hypercholesterolemia and premature atherosclerosis. Despite the significance of this interaction for cholesterol homeostasis, no structure of either ARH or the LDLR tail is available to determine its molecular basis. We report the crystal structure at 1.37-Å resolution of the phosphotyrosine-binding (PTB) domain of ARH in complex with an LDLR tail peptide containing the FxNPxY(0) internalization signal. Surprisingly, ARH interacts with a longer portion of the tail than previously recognized, which extends to I(-7)xF(-5)xNPxY(0)QK(+2). The LDLR tail assumes a unique "Hook"-like structure with a double β-turn conformation, which is accommodated in distinctive ARH structural determinants (i.e., an extended backbone hydrogen-bonding platform, three hydrophobic helical grooves, and a hydrophobic pocket for Y(0)). This unique complementarity differs significantly in related PTB proteins and may account for the unique physiological role of these partners in the hepatic uptake of cholesterol LDL. Moreover, the unusual hydrophobic pocket for Y(0) explains the distinctive ability of ARH to internalize proteins containing either FxNPxY(0) or FxNPxF(0) sequences. Biophysical measurements reveal how mutations associated with hypercholesterolemia destabilize ARH and its complex with LDLR and illuminate LDL internalization defects seen in patients.


    Organizational Affiliation

    Division of Cell Biology, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
LDL receptor adaptor proteinA137Rattus norvegicusMutation(s): 0 
Gene Names: Ldlrap1RGD1563417_predictedrCG_31034Arh
Find proteins for D3ZAR1 (Rattus norvegicus)
Explore D3ZAR1 
Go to UniProtKB:  D3ZAR1
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Low-density lipoprotein receptorB [auth Q]14Homo sapiensMutation(s): 0 
Gene Names: LDLR
Find proteins for P01130 (Homo sapiens)
Explore P01130 
Go to UniProtKB:  P01130
NIH Common Fund Data Resources
PHAROS:  P01130
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.37 Å
  • R-Value Free: 0.206 
  • R-Value Work: 0.151 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 29.097α = 90
b = 59.095β = 90
c = 77.083γ = 90
Software Package:
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Blu-Icedata collection

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2011-06-29 
  • Released Date: 2012-04-18 
  • Deposition Author(s): Dvir, H., Zajonc, D.M.

Revision History  (Full details and data files)

  • Version 1.0: 2012-04-18
    Type: Initial release
  • Version 1.1: 2012-05-02
    Changes: Database references
  • Version 1.2: 2012-05-16
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description