The Crystal structure of the Carbohydrate recognition domain of the glycoprotein sorting receptor p58/ERGIC-53 reveals a novel metal binding site and conformational changes associated with calcium ion binding

Experimental Data Snapshot

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 

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The Crystal Structure of the Carbohydrate-recognition Domain of the Glycoprotein Sorting Receptor p58/ERGIC-53 Reveals an Unpredicted Metal-binding Site and Conformational Changes Associated with Calcium Ion Binding.

Velloso, L.M.Svensson, K.Pettersson, R.F.Lindqvist, Y.

(2003) J Mol Biol 334: 845-851

  • DOI: https://doi.org/10.1016/j.jmb.2003.10.031
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    p58/ERGIC-53 is a calcium-dependent animal lectin that acts as a cargo receptor, binding to a set of glycoproteins in the endoplasmic reticulum (ER) and transporting them to the Golgi complex. It is similar in structure to calcium-dependent leguminous lectins. We have determined the structure of the carbohydrate-recognition domain of p58/ERGIC-53 in its calcium-bound form. The structure reveals localized but large conformational changes in relation to the previously determined metal ion-free structure, mapping mostly to the ligand-binding site. It reveals the presence of two calcium ion-binding sites located 6A apart, one of which has no equivalent in the plant lectins. The second metal ion-binding site present in that class of lectins, binding Mn(2+), is absent from p58/ERGIC-53. The absence of a short loop in the ligand-binding site in this protein suggests that it has adapted to optimally bind the high-mannose Man(8)(GlcNAc)(2) glycan common to glycoproteins at the ER exit stage.

  • Organizational Affiliation

    Molecular Structural Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, S-171 77 Stockholm, Sweden.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ERGIC-53 protein
A, B, C, D
263Rattus norvegicusMutation(s): 0 
Gene Names: LMAN1 OR ERGIC53
Find proteins for Q62902 (Rattus norvegicus)
Explore Q62902 
Go to UniProtKB:  Q62902
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ62902
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.40 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.223 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.351α = 91.05
b = 81.068β = 94.14
c = 82.306γ = 94.99
Software Package:
Software NamePurpose
MOSFLMdata reduction
CCP4data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-12-16
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2023-08-23
    Changes: Data collection, Database references, Derived calculations, Refinement description