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 

wwPDB Validation 3D Report Full Report


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
  • Structures With Same Primary Citation

  • 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 an ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Glypican-1A, B, C, D526Homo sapiensMutation(s): 3 
Gene Names: GPC1
Find proteins for P35052 (Homo sapiens)
Explore P35052 
Go to UniProtKB:  P35052
NIH Common Fund Data Resources
PHAROS  P35052
GTEx  ENSG00000063660
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download CCD File 
A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N		 Ligand Interaction
CA
Query on CA
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N		 Ligand Interaction
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 

  • 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