4C9F

Structure of SIGN-R1 in complex with Sulfodextran


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural Basis for Selective Recognition of Endogenous and Microbial Polysaccharides by Macrophage Receptor Sign-R1

Silva-Martin, N.Bartual, S.G.Rodriguez, A.Ramirez, E.Chacon, P.Anthony, R.M.Park, C.G.Hermoso, J.A.

(2014) Structure 22: 1595

  • DOI: 10.1016/j.str.2014.09.001
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • SIGN-R1 is a principal receptor for microbial polysaccharides uptake and is responsible for C3 fixation via an unusual complement activation pathway on splenic marginal zone macrophages. In these macrophages, SIGN-R1 is also involved in anti-inflamma ...

    SIGN-R1 is a principal receptor for microbial polysaccharides uptake and is responsible for C3 fixation via an unusual complement activation pathway on splenic marginal zone macrophages. In these macrophages, SIGN-R1 is also involved in anti-inflammatory activity of intravenous immunoglobulin by direct interaction with sialylated Fcs. The high-resolution crystal structures of SIGN-R1 carbohydrate recognition domain and its complexes with dextran sulfate or sialic acid, and of the sialylated Fc antibody provide insights into SIGN-R1’s selective recognition of a-2,6-sialylated glycoproteins. Unexpectedly, an additional binding site has been found in the SIGNR1 carbohydrate recognition domain, structurally separate from the calcium-dependent carbohydrate-binding site. This secondary binding site could bind repetitive molecular patterns, as observed in microbial polysaccharides, in a calcium-independent manner. These two binding sites may allow SIGNR1 to simultaneously bind both immune glycoproteins and microbial polysaccharide components, accommodating SIGN-R1’s ability to relate the recognition of microbes to the activation of the classical complement pathway.


    Organizational Affiliation

    Membrane Protein Disease Research Group, Department of Biochemistry, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Alberta, Canada T6G 2H7.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
CD209 ANTIGEN-LIKE PROTEIN B
A, B, C, D
134Mus musculusMutation(s): 0 
Gene Names: Cd209b
Find proteins for Q8CJ91 (Mus musculus)
Go to UniProtKB:  Q8CJ91
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GQ4
Query on GQ4

Download CCD File 
C
alpha-D-glucopyranosyl-(1->6)-alpha-D-glucopyranosyl-(1->6)-alpha-D-glucopyranosyl-(1->6)-4-O-sulfo-alpha-D-glucopyranose
C24 H42 O24 S
YGYJHMTXBVYBPR-QBHJDJPESA-N
 Ligand Interaction
GQ2
Query on GQ2

Download CCD File 
A, B
6-O-alpha-D-glucopyranosyl-4-O-sulfo-alpha-D-glucopyranose
C12 H22 O14 S
PHBNZSXYHCHLCJ-MFRLZQSSSA-N
 Ligand Interaction
GQ1
Query on GQ1

Download CCD File 
D
4-O-sulfo-alpha-D-glucopyranose
C6 H12 O9 S
LOTQRUGOUKUSEY-UKFBFLRUSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, B, C, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.233 
  • R-Value Work: 0.191 
  • R-Value Observed: 0.193 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.025α = 90
b = 97.959β = 120.86
c = 73.846γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-10-15
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Database references
  • Version 1.2: 2015-02-25
    Changes: Database references