1URL | pdb_00001url

N-TERMINAL DOMAIN OF SIALOADHESIN (MOUSE) IN COMPLEX WITH GLYCOPEPTIDE

• PDB DOI: https://doi.org/10.2210/pdb1URL/pdb

• Classification: SUGAR BINDING PROTEIN/IMMUNE SYSTEM
• Organism(s): Mus musculus, synthetic construct
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2003-10-31 Released: 2004-10-20 
• Deposition Author(s): Bukrinsky, J.T., Hilaire, P.M.S., Meldal, M., Crocker, P.R., Henriksen, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.273 (Depositor), 0.296 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.243 (DCC) 
• R-Value Observed: 
  0.225 (Depositor) 

Starting Model: experimental

Literature

Complex of Sialoadhesin with a Glycopeptide Ligand

Bukrinsky, J.T., Hilaire, P.M.S., Meldal, M., Crocker, P.R., Henriksen, A.

(2004) Biochim Biophys Acta 1702: 173

• PubMed: 15488769 
• DOI: https://doi.org/10.1016/j.bbapap.2004.08.015
• Primary Citation Related Structures: 
  1URL


• PubMed Abstract: 
  

  Sialoadhesin is a sialic acid-binding immunoglobulin-like lectin (Siglec), expressed on subsets of macrophages. It is a model system for Siglec receptor-mediated cell surface interactions through binding of sialylated glycoconjugates. The N-terminal sialoadhesin domain can mediate sialic acid-binding on its own. The structure of this domain has been determined in complex with a sialic acid-containing heptapeptide, (Ala-Gly-His-Thr(Neu5Ac)-Trp-Gly-His). The affinity of sialoadhesin for this ligand is four times higher than the affinity for the natural linkage 2,3'-sialyllactose. The structure of the glycopeptide complex suggests strategies for ligand optimization and provides possible explanations for the observed differences in specificities among the Siglecs.

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Organizational Affiliation: 
• Department of Chemistry, The Carlsberg Laboratory, Gamle Carlsberg Vej 10, DK-2500 Valby, Denmark.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 14.28 kDa 
• Atom Count: 1,004 
• Modeled Residue Count: 124 
• Deposited Residue Count: 125 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SIALOADHESIN	A	118	Mus musculus	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q62230 (Mus musculus) Explore Q62230  Go to UniProtKB:  Q62230
IMPC:  MGI:99668

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
ALA-GLY-HIS-THR-TRP-GLY-HIA	B	7	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SIA	C [auth B]	N-acetyl-alpha-neuraminic acid C11 H19 N O9 SQVRNKJHWKZAKO-YRMXFSIDSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HIA	B	L-PEPTIDE LINKING	C6 H10 N4 O		HIS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.273 (Depositor), 0.296 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.243 (DCC) 
• R-Value Observed: 0.225 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.23	α = 90
b = 78.46	β = 90
c = 34.22	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
MOSFLM	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2004-10-20 
Deposition Author(s): Bukrinsky, J.T., Hilaire, P.M.S., Meldal, M., Crocker, P.R., Henriksen, A.

Revision History  

• Version 1.0: 2004-10-20
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2018-01-17
  Changes: Data collection, Source and taxonomy
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary