1H8U

Crystal Structure of the Eosinophil Major Basic Protein at 1.8A: An Atypical Lectin with a Paradigm Shift in Specificity


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history


Literature

Crystal Structure of the Eosinophil Major Basic Protein at 1.8A. An Atypical Lectin with a Paradigm Shift in Specificity

Swaminathan, G.J.Weaver, A.J.Loegering, D.A.Checkel, J.L.Leonidas, D.D.Gleich, G.J.Acharya, K.R.

(2001) J Biol Chem 276: 26197

  • DOI: https://doi.org/10.1074/jbc.M100848200
  • Primary Citation of Related Structures:  
    1H8U

  • PubMed Abstract: 

    The eosinophil major basic protein (EMBP) is the predominant constituent of the crystalline core of the eosinophil primary granule. EMBP is directly implicated in epithelial cell damage, exfoliation, and bronchospasm in allergic diseases such as asthma. Here we report the crystal structure of EMBP at 1.8 A resolution, and show that it is similar to that of members of the C-type lectin superfamily with which it shares minimal amino acid sequence identity (approximately 15--28%). However, this protein lacks a Ca(2+)/carbohydrate-binding site. Our analysis suggests that EMBP specifically binds heparin. Based on our results, we propose a possible new function for this protein, which is likely to have implications for EMBP function.


  • Organizational Affiliation

    Department of Biology and Biochemistry, University of Bath, Claverton Down, Bath BA2 7AY, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
EOSINOPHIL GRANULE MAJOR BASIC PROTEIN 1
A, B
117Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P13727 (Homo sapiens)
Explore P13727 
Go to UniProtKB:  P13727
PHAROS:  P13727
GTEx:  ENSG00000186652 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP13727
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
F [auth A]
G [auth A]
C [auth A],
D [auth A],
E [auth A],
F [auth A],
G [auth A],
J [auth B],
K [auth B],
L [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.234 
  • R-Value Observed: 0.234 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 74.328α = 90
b = 57.487β = 113.2
c = 60.961γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-07-17
    Type: Initial release
  • Version 1.1: 2011-05-07
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-12-13
    Changes: Data collection, Database references, Refinement description