1XFE | pdb_00001xfe

Solution structure of the LA7-EGFA pair from the LDL receptor


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 43 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

wwPDB Validation 3D Report Full Report

Validation slider image for 1XFE

This is version 1.4 of the entry. See complete history

Literature

Cooperation between Fixed and Low pH-Inducible Interfaces Controls Lipoprotein Release by the LDL Receptor

Beglova, N.Jeon, H.Fisher, C.Blacklow, S.C.

(2004) Mol Cell 16: 281-292

  • DOI: https://doi.org/10.1016/j.molcel.2004.09.038
  • Primary Citation Related Structures: 
    1XFE

  • PubMed Abstract: 

    Low-density lipoprotein (LDL) receptors bind lipoprotein particles at the cell surface and release them in the low pH environment of the endosome. The published structure of the receptor determined at endosomal pH reveals an interdomain interface between its beta propeller and its fourth and fifth ligand binding (LA) repeats, suggesting that the receptor adopts a closed conformation at low pH to release LDL. Here, we combine lipoprotein binding and release assays with NMR spectroscopy to examine structural features of the receptor promoting release of LDL at low pH. These studies lead to a model in which the receptor uses a pH-invariant scaffold as an anchor to restrict conformational search space, combining it with flexible linkers between ligand binding repeats to interconvert between open and closed conformations. This finely tuned balance between interdomain rigidity and flexibility is likely to represent a shared structural feature in proteins of the LDL receptor family.


  • Organizational Affiliation
    • Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.

Macromolecule Content 

  • Total Structure Weight: 9.3 kDa 
  • Atom Count: 635 
  • Modeled Residue Count: 83 
  • Deposited Residue Count: 83 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Low-density lipoprotein receptor83Homo sapiensMutation(s): 0 
Gene Names: LDLR
UniProt & NIH Common Fund Data Resources
Find proteins for P01130 (Homo sapiens)
Explore P01130 
Go to UniProtKB:  P01130
PHAROS:  P01130
GTEx:  ENSG00000130164 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP01130
Sequence Annotations
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Reference Sequence

Small Molecules

Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 43 
  • Conformers Submitted: 15 
  • Selection Criteria: structures with the lowest energy 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-11-02
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2022-03-02
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-10-30
    Changes: Data collection, Structure summary