4YWT

Crystal structure of full-length glypican-1 core protein after controlled crystal dehydration to 87% relative humidity

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 

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This is version 1.5 of the entry. See complete history. 


Literature

Structural Aspects of N-Glycosylations and the C-terminal Region in Human Glypican-1.

Awad, W., Adamczyk, B., Ornros, J., Karlsson, N.G., Mani, K., Logan, D.T.

(2015) J Biol Chem 290: 22991-23008

  • DOI: 10.1074/jbc.M115.660878
  • Primary Citation of Related Structures:  
    4YWT

  • PubMed Abstract: 

    • Glypicans are multifunctional cell surface proteoglycans involved in several important cellular signaling pathways. Glypican-1 (Gpc1) is the predominant heparan sulfate proteoglycan in the developing and adult human brain. The two N-linked glycans and the C-terminal domain that attach the core protein to the cell membrane are not resolved in the Gpc1 crystal structure ...

    Glypicans are multifunctional cell surface proteoglycans involved in several important cellular signaling pathways. Glypican-1 (Gpc1) is the predominant heparan sulfate proteoglycan in the developing and adult human brain. The two N-linked glycans and the C-terminal domain that attach the core protein to the cell membrane are not resolved in the Gpc1 crystal structure. Therefore, we have studied Gpc1 using crystallography, small angle x-ray scattering, and chromatographic approaches to elucidate the composition, structure, and function of the N-glycans and the C terminus and also the topology of Gpc1 with respect to the membrane. The C terminus is shown to be highly flexible in solution, but it orients the core protein transverse to the membrane, directing a surface evolutionarily conserved in Gpc1 orthologs toward the membrane, where it may interact with signaling molecules and/or membrane receptors on the cell surface, or even the enzymes involved in heparan sulfate substitution in the Golgi apparatus. Furthermore, the N-glycans are shown to extend the protein stability and lifetime by protection against proteolysis and aggregation.

    Related Citations: 
    • Improvements in the order, isotropy and electron density of glypican-1 crystals by controlled dehydration.
      Awad, W., Svensson Birkedal, G., Thunnissen, M.M., Mani, K., Logan, D.T.
      (2013) Acta Crystallogr D Biol Crystallogr 69: 2524
    • Crystal structure of N-glycosylated human glypican-1 core protein: structure of two loops evolutionarily conserved in vertebrate glypican-1.
      Svensson, G., Awad, W., Hakansson, M., Mani, K., Logan, D.T.
      (2012) J Biol Chem 287: 14040
    Organizational Affiliation: 

    From the Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, SE-221 00 Lund, derek.logan@biochemistry.lu.se.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glypican-1A, B, C, D526Homo sapiensMutation(s): 3 
Gene Names: GPC1
UniProt & NIH Common Fund Data Resources
Find proteins for P35052 (Homo sapiens)
Explore P35052 
Go to UniProtKB:  P35052
PHAROS:  P35052
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35052
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.38 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.239 
  • R-Value Observed: 0.240 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.78α = 90
b = 166.59β = 90.38
c = 137.7γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-29
    Type: Initial release
  • Version 1.1: 2015-08-05
    Changes: Database references
  • Version 1.2: 2015-09-30
    Changes: Database references
  • Version 1.3: 2018-01-17
    Changes: Data collection
  • Version 1.4: 2019-04-03
    Changes: Data collection, Source and taxonomy
  • Version 1.5: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary