2YD6

Crystal structure of the N-terminal Ig1-2 module of Human Receptor Protein Tyrosine Phosphatase Delta

• PDB DOI:  https://doi.org/10.2210/pdb2YD6/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2011-03-17 Released: 2011-04-13 
• Deposition Author(s): Coles, C.H., Shen, Y., Tenney, A.P., Siebold, C., Sutton, G.C., Lu, W., Gallagher, J.T., Jones, E.Y., Flanagan, J.G., Aricescu, A.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.171 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 

Literature

Proteoglycan-Specific Molecular Switch for Rptp Sigma Clustering and Neuronal Extension.

Coles, C.H., Shen, Y., Tenney, A.P., Siebold, C., Sutton, G.C., Lu, W., Gallagher, J.T., Jones, E.Y., Flanagan, J.G., Aricescu, A.R.

(2011) Science 332: 484

• PubMed: 21454754 
• DOI: https://doi.org/10.1126/science.1200840
• Primary Citation of Related Structures:  
  2YD1, 2YD2, 2YD3, 2YD4, 2YD5, 2YD6, 2YD7, 2YD8, 2YD9


• PubMed Abstract: 
  

Heparan and chondroitin sulfate proteoglycans (HSPGs and CSPGs, respectively) regulate numerous cell surface signaling events, with typically opposite effects on cell function. CSPGs inhibit nerve regeneration through receptor protein tyrosine phosphatase sigma (RPTPσ). Here we report that RPTPσ acts bimodally in sensory neuron extension, mediating CSPG inhibition and HSPG growth promotion. Crystallographic analyses of a shared HSPG-CSPG binding site reveal a conformational plasticity that can accommodate diverse glycosaminoglycans with comparable affinities. Heparan sulfate and analogs induced RPTPσ ectodomain oligomerization in solution, which was inhibited by chondroitin sulfate. RPTPσ and HSPGs colocalize in puncta on sensory neurons in culture, whereas CSPGs occupy the extracellular matrix. These results lead to a model where proteoglycans can exert opposing effects on neuronal extension by competing to control the oligomerization of a common receptor.

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Organizational Affiliation: 

Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content

• Total Structure Weight: 23.7 kDa 
• Atom Count: 1,925 
• Modelled Residue Count: 195 
• Deposited Residue Count: 212 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PTPRD PROTEIN	A	212	Homo sapiens	Mutation(s): 0  Gene Names: PTPRD EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P23468 (Homo sapiens) Explore P23468  Go to UniProtKB:  P23468
PHAROS:  P23468

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
CL	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.35 Å
• R-Value Free: 0.171 
• R-Value Work: 0.141 
• R-Value Observed: 0.142 
• Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.71	α = 90
b = 48.71	β = 90
c = 145.91	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
XDS	data reduction
xia2	data scaling
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-04-13 
Deposition Author(s): Coles, C.H., Shen, Y., Tenney, A.P., Siebold, C., Sutton, G.C., Lu, W., Gallagher, J.T., Jones, E.Y., Flanagan, J.G., Aricescu, A.R.

Revision History  

• Version 1.0: 2011-04-13
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance