4U7M | pdb_00004u7m

LRIG1 extracellular domain: Structure and Function Analysis

  • Classification: SIGNALING PROTEIN
  • Organism(s): Homo sapiens
  • Expression System: Spodoptera frugiperda
  • Mutation(s): No 

  • Deposited: 2014-07-31 Released: 2015-04-08 
  • Deposition Author(s): Xu, Y.
  • Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free: 
    0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work: 
    0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 
    0.207 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 4U7M

Ligand Structure Quality Assessment 


This is version 1.6 of the entry. See complete history

Literature

LRIG1 Extracellular Domain: Structure and Function Analysis.

Xu, Y.Soo, P.Walker, F.Zhang, H.H.Redpath, N.Tan, C.W.Nicola, N.A.Adams, T.E.Garrett, T.P.Zhang, J.G.Burgess, A.W.

(2015) J Mol Biology 427: 1934-1948

  • DOI: https://doi.org/10.1016/j.jmb.2015.03.001
  • Primary Citation Related Structures: 
    4U7L, 4U7M

  • PubMed Abstract: 

    We have expressed and purified three soluble fragments of the human LRIG1-ECD (extracellular domain): the LRIG1-LRR (leucine-rich repeat) domain, the LRIG1-3Ig (immunoglobulin-like) domain, and the LRIG1-LRR-1Ig fragment using baculovirus vectors in insect cells. The two LRIG1 domains crystallised so that we have been able to determine the three-dimensional structures at 2.3Å resolution. We developed a three-dimensional structure for the LRIG1-ECD using homology modelling based on the LINGO-1 structure. The LRIG1-LRR domain and the LRIG1-LRR-1Ig fragment are monomers in solution, whereas the LRIG1-3Ig domain appears to be dimeric. We could not detect any binding of the LRIG1 domains or the LRIG1-LRR-1Ig fragment to the EGF receptor (EGFR), either in solution using biosensor analysis or when the EGFR was expressed on the cell surface. The FLAG-tagged LRIG1-LRR-1Ig fragment binds weakly to colon cancer cells regardless of the presence of EGFRs. Similarly, neither the soluble LRIG1-LRR nor the LRIG1-3Ig domains nor the full-length LRIG1 co-expressed in HEK293 cells inhibited ligand-stimulated activation of cell-surface EGFR.


  • Organizational Affiliation
    • Structural Biology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia; Cancer and Haematology Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria 3052, Australia.

Macromolecule Content 

  • Total Structure Weight: 32.65 kDa 
  • Atom Count: 2,264 
  • Modeled Residue Count: 289 
  • Deposited Residue Count: 293 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Leucine-rich repeats and immunoglobulin-like domains protein 1293Homo sapiensMutation(s): 0 
Gene Names: LRIG1LIG1
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JA1 (Homo sapiens)
Explore Q96JA1 
Go to UniProtKB:  Q96JA1
PHAROS:  Q96JA1
GTEx:  ENSG00000144749 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JA1
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q96JA1-1
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG



Download:Ideal Coordinates CCD File
B [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.76 Å
  • R-Value Free:  0.253 (Depositor), 0.255 (DCC) 
  • R-Value Work:  0.205 (Depositor), 0.213 (DCC) 
  • R-Value Observed: 0.207 (Depositor) 
Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.04α = 90
b = 121.04β = 90
c = 115.8γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data

  • Released Date: 2015-04-08 
  • Deposition Author(s): Xu, Y.

Funding OrganizationLocationGrant Number
National Health and Medical Research Council (NHMRC, Australia)Australia487922

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-05-13
    Changes: Database references
  • Version 1.2: 2017-09-20
    Changes: Author supporting evidence, Data collection, Database references, Derived calculations, Source and taxonomy
  • Version 1.3: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description, Structure summary
  • Version 1.6: 2024-10-23
    Changes: Structure summary