Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Biological Assembly 3  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 3 assigned by authors and generated by PISA (software)

Biological Assembly 4  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 4 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 235.27 kDa 
• Atom Count: 13110 
• Modelled Residue Count: 1671 
• Deposited Residue Count: 2104 
• Unique protein chains: 1

4YWT

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

• DOI: 10.2210/pdb4YWT/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): Yes 


• Deposited: 2015-03-21 Released: 2015-07-29 
• Deposition Author(s): Awad, W., Mani, K., Logan, D.T.

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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 

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

• PubMed: 26203194 
• 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. 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.

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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

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Organizational Affiliation: 

From the Department of Biochemistry and Structural Biology, Centre for Molecular Protein Science, Lund University, Box 124, SE-221 00 Lund, [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glypican-1	A, B, C, D	526	Homo sapiens	Mutation(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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	E [auth A], H [auth B], K [auth C], O [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	F [auth A],  G [auth A],  I [auth B],  J [auth B],  L [auth C],  M [auth C],  N [auth C],  P [auth D],  Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 46.78	α = 90
b = 166.59	β = 90.38
c = 137.7	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-03-21 
• Released Date: 2015-07-29 
Deposition Author(s): Awad, W., Mani, K., Logan, D.T.

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