2YD9 | pdb_00002yd9

Crystal structure of the N-terminal Ig1-3 module of Human Receptor Protein Tyrosine Phosphatase Sigma

• PDB DOI: https://doi.org/10.2210/pdb2YD9/pdb

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


• Deposited: 2011-03-18 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: 2.60 Å
• R-Value Free: 
  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work: 
  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

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 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  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 34.64 kDa 
• Atom Count: 2,198 
• Modeled Residue Count: 278 
• Deposited Residue Count: 304 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE S	A	304	Homo sapiens	Mutation(s): 2  EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q13332 (Homo sapiens) Explore Q13332  Go to UniProtKB:  Q13332
PHAROS:  Q13332 GTEx:  ENSG00000105426
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q13332-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
B3P	L [auth A]	2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C11 H26 N2 O6 HHKZCCWKTZRCCL-UHFFFAOYSA-N
NAG	J [auth A], K [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IOD	F [auth A], G [auth A], H [auth A], I [auth A]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M
CL	B [auth A], C [auth A], D [auth A], E [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.289 (Depositor), 0.292 (DCC) 
• R-Value Work:  0.247 (Depositor), 0.248 (DCC) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.699	α = 90
b = 90.043	β = 90
c = 143.283	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	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
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.4: 2023-12-20
  Changes: Data collection, Database references, Refinement description, Structure summary
• Version 1.5: 2024-11-20
  Changes: Structure summary