2BRS

EMBP Heparin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 

wwPDB Validation   3D Report Full Report


This is version 2.1 of the entry. See complete history


Literature

Eosinophil-Granule Major Basic Protein, a C-Type Lectin, Binds Heparin

Swaminathan, G.J.Myszka, D.G.Katsamba, P.S.Ohnuki, L.E.Gleich, G.J.Acharya, K.R.

(2005) Biochemistry 44: 14152

  • DOI: https://doi.org/10.1021/bi051112b
  • Primary Citation of Related Structures:  
    2BRS

  • PubMed Abstract: 

    The eosinophil major basic protein (EMBP), a constituent of the eosinophil secondary granule, is implicated in cytotoxicity and mediation of allergic disorders such as asthma. It is a member of the C-type lectin family, but lacks a Ca(2+)- and carbohydrate-binding site as seen in other members of this family. Here, we report the crystal structure of EMBP in complex with a heparin disaccharide and in the absence of Ca(2+), the first such report of any C-lectin with this sugar. We also provide direct evidence of binding of EMBP to heparin and heparin disaccharide by surface plasmon resonance. We propose that the sugars recognized by EMBP are likely to be proteoglycans such as heparin, leading to new interpretations 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
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
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-O-sulfo-beta-L-altropyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan:  G88021JE
GlyCosmos:  G88021JE
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 75.913α = 90
b = 57.917β = 111.85
c = 61.831γ = 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: 2005-10-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
  • Version 2.1: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary