2BRS

EMBP Heparin complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 

wwPDB Validation 3D Report Full Report


This is version 1.2 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: 10.1021/bi051112b

  • 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 carboh ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
EOSINOPHIL-GRANULE MAJOR BASIC PROTEIN
A, B
117Homo sapiensMutation(s): 0 
Gene Names: PRG2 (MBP)
Find proteins for P13727 (Homo sapiens)
Go to Gene View: PRG2
Go to UniProtKB:  P13727
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
SGN
Query on SGN

Download SDF File 
Download CCD File 
A
N,O6-DISULFO-GLUCOSAMINE
C6 H13 N O11 S2
DQTRACMFIGDHSN-UKFBFLRUSA-N
 Ligand Interaction
IDU
Query on IDU

Download SDF File 
Download CCD File 
A
2-O-sulfo-beta-L-altropyranuronic acid
C6 H10 O10 S
COJBCAMFZDFGFK-TVSWGBMESA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.291 
  • R-Value Work: 0.247 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 75.913α = 90.00
b = 57.917β = 111.85
c = 61.831γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNSrefinement
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-10-26
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance