N-terminal 3 domains of CI-MPR bound to mannose 6-phosphate

Experimental Data Snapshot

  • Resolution: 2.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 

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This is version 2.1 of the entry. See complete history


The N-terminal carbohydrate recognition site of the cation-independent mannose 6-phosphate receptor

Olson, L.J.Dahms, N.M.Kim, J.-J.P.

(2004) J Biol Chem 279: 34000-34009

  • DOI: https://doi.org/10.1074/jbc.M404588200
  • Primary Citation of Related Structures:  
    1SYO, 1SZ0

  • PubMed Abstract: 

    The 300-kDa cation-independent mannose 6-phosphate receptor (CI-MPR) plays a critical role in the trafficking of newly synthesized mannose 6-phosphate-containing acid hydrolases to the lysosome. The receptor contains two high affinity carbohydrate recognition sites within its 15-domain extracytoplasmic region, with essential residues for carbohydrate recognition located in domain 3 and domain 9. Previous studies have shown that these two sites are distinct with respect to carbohydrate specificity. In addition, expression of truncated forms of the CI-MPR demonstrated that domain 9 can be expressed as an isolated domain, retaining high affinity (Kd approximately 1 nm) carbohydrate binding, whereas expression of domain 3 alone resulted in a protein capable of only low affinity binding (Kd approximately 1 microm) toward a lysosomal enzyme. In the current report the crystal structure of the N-terminal 432 residues of the CI-MPR, encompassing domains 1-3, was solved in the presence of bound mannose 6-phosphate. The structure reveals the unique architecture of this carbohydrate binding pocket and provides insight into the ability of this site to recognize a variety of mannose-containing sugars.

  • Organizational Affiliation

    Department of Biochemistry, Medical College of Wisconsin, Milwaukee, Wisconsin 53226, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
cation-independent mannose 6-phosphate receptor
A, B
432Bos taurusMutation(s): 0 
Gene Names: IGF2RM6P
Find proteins for P08169 (Bos taurus)
Explore P08169 
Go to UniProtKB:  P08169
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08169
Sequence Annotations
  • Reference Sequence


Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
Glycosylation Resources
GlyTouCan:  G65996GC
GlyCosmos:  G65996GC
GlyGen:  G65996GC
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
M6P PDBBind:  1SYO Kd: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.228 
  • R-Value Observed: 0.228 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 61.4α = 90
b = 86.4β = 108.8
c = 86.9γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2004-06-29
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, 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: 2023-08-23
    Changes: Data collection, Database references, Refinement description, Structure summary