1DQO | pdb_00001dqo

Crystal structure of the cysteine rich domain of mannose receptor complexed with Acetylgalactosamine-4-sulfate

• PDB DOI: https://doi.org/10.2210/pdb1DQO/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Mus musculus
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2000-01-04 Released: 2000-05-10 
• Deposition Author(s): Liu, Y., Chirino, A.J., Misulovin, Z., Leteux, C., Feizi, T., Nussenzweig, M.C., Bjorkman, P.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.232 (Depositor) 
• R-Value Work: 
  0.211 (Depositor) 
• R-Value Observed: 
  0.213 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the cysteine-rich domain of mannose receptor complexed with a sulfated carbohydrate ligand.

Liu, Y., Chirino, A.J., Misulovin, Z., Leteux, C., Feizi, T., Nussenzweig, M.C., Bjorkman, P.J.

(2000) J Exp Medicine 191: 1105-1116

• PubMed: 10748229 
• DOI: https://doi.org/10.1084/jem.191.7.1105
• Primary Citation Related Structures: 
  1DQG, 1DQO


• PubMed Abstract: 
  

  The macrophage and epithelial cell mannose receptor (MR) binds carbohydrates on foreign and host molecules. Two portions of MR recognize carbohydrates: tandemly arranged C-type lectin domains facilitate carbohydrate-dependent macrophage uptake of infectious organisms, and the NH(2)-terminal cysteine-rich domain (Cys-MR) binds to sulfated glycoproteins including pituitary hormones. To elucidate the mechanism of sulfated carbohydrate recognition, we determined crystal structures of Cys-MR alone and complexed with 4-sulfated-N-acetylgalactosamine at 1.7 and 2.2 A resolution, respectively. Cys-MR folds into an approximately three-fold symmetric beta-trefoil shape resembling fibroblast growth factor. The sulfate portions of 4-sulfated-N-acetylgalactosamine and an unidentified ligand found in the native crystals bind in a neutral pocket in the third lobe. We use the structures to rationalize the carbohydrate binding specificities of Cys-MR and compare the recognition properties of Cys-MR with other beta-trefoil proteins.

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Organizational Affiliation: 
• Division of Biology 156-29, California Institute of Technology, Pasadena, California 91125, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.86 kDa 
• Atom Count: 1,256 
• Modeled Residue Count: 134 
• Deposited Residue Count: 135 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MANNOSE RECEPTOR	A	135	Mus musculus	Mutation(s): 0
UniProt
Find proteins for Q61830 (Mus musculus) Explore Q61830  Go to UniProtKB:  Q61830

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ASG	B [auth A]	2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose C8 H15 N O9 S WHCJUIFHMJFEFZ-UIAUGNHASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.232 (Depositor) 
• R-Value Work:  0.211 (Depositor) 
• R-Value Observed: 0.213 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.43	α = 90
b = 41.48	β = 90
c = 100.3	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2000-05-10 
Deposition Author(s): Liu, Y., Chirino, A.J., Misulovin, Z., Leteux, C., Feizi, T., Nussenzweig, M.C., Bjorkman, P.J.

Revision History  

• Version 1.0: 2000-05-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  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, Structure summary
• Version 2.1: 2023-08-09
  Changes: Advisory, Data collection, Database references, Refinement description, Structure summary
• Version 2.2: 2024-11-13
  Changes: Structure summary