6TPV

Crystal structures of FNIII domain one and two of the human leucocyte common antigen-related protein, LAR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 

Starting Model: experimental
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This is version 1.1 of the entry. See complete history


Literature

Crystal and solution structures of fragments of the human leucocyte common antigen-related protein.

Vilstrup, J.Simonsen, A.Birkefeldt, T.Strandbygard, D.Lyngso, J.Pedersen, J.S.Thirup, S.

(2020) Acta Crystallogr D Struct Biol 76: 406-417

  • DOI: https://doi.org/10.1107/S2059798320003885
  • Primary Citation of Related Structures:  
    6TPT, 6TPU, 6TPV, 6TPW

  • PubMed Abstract: 

    Leucocyte common antigen-related protein (LAR) is a post-synaptic type I transmembrane receptor protein that is important for neuronal functionality and is genetically coupled to neuronal disorders such as attention deficit hyperactivity disorder (ADHD). To understand the molecular function of LAR, structural and biochemical studies of protein fragments derived from the ectodomain of human LAR have been performed. The crystal structure of a fragment encompassing the first four FNIII domains (LAR FN1-4 ) showed a characteristic L shape. SAXS data suggested limited flexibility within LAR FN1-4 , while rigid-body refinement of the SAXS data using the X-ray-derived atomic model showed a smaller angle between the domains defining the L shape compared with the crystal structure. The capabilities of the individual LAR fragments to interact with heparin was examined using microscale thermophoresis and heparin-affinity chromatography. The results showed that the three N-terminal immunoglobulin domains (LAR Ig1-3 ) and the four C-terminal FNIII domains (LAR FN5-8 ) both bound heparin, while LAR FN1-4 did not. The low-molecular-weight heparin drug Innohep induced a shift in hydrodynamic volume as assessed by size-exclusion chromatography of LAR Ig1-3 and LAR FN5-8 , while the chemically defined pentameric heparin drug Arixtra did not. Together, the presented results suggest the presence of an additional heparin-binding site in human LAR.


  • Organizational Affiliation

    Department of Molecular Biology and Genetics, Center for Structural Biology, Aarhus University, Gustav Wieds Vej 10C, 8000 Aarhus C, Denmark.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Receptor-type tyrosine-protein phosphatase F
A, B
208Homo sapiensMutation(s): 0 
Gene Names: PTPRFLAR
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P10586 (Homo sapiens)
Explore P10586 
Go to UniProtKB:  P10586
PHAROS:  P10586
GTEx:  ENSG00000142949 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP10586
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
C [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.27α = 90
b = 50.843β = 97.22
c = 65.525γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
LundbeckfondenDenmarkR198-2015-168
Novo Nordisk FoundationDenmarkDFF 4183-00604

Revision History  (Full details and data files)

  • Version 1.0: 2020-05-13
    Type: Initial release
  • Version 1.1: 2024-01-24
    Changes: Data collection, Database references, Refinement description