Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 83.29 kDa 
• Atom Count: 4523 
• Residue Count: 564 
• Unique protein chains: 1

2V5Y

Crystal structure of the receptor protein tyrosine phosphatase mu ectodomain

• DOI: 10.2210/pdb2V5Y/pdb

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


• Deposited: 2007-07-11 Released: 2007-09-11 
• Deposition Author(s): Aricescu, A.R., Siebold, C., Choudhuri, K., Chang, V.T., Lu, W., Davis, S.J., van der Merwe, P.A., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.320 
• R-Value Work: 0.242 
• R-Value Observed: 0.246 

Literature

Structure of a Tyrosine Phosphatase Adhesive Interaction Reveals a Spacer-Clamp Mechanism.

Aricescu, A.R., Siebold, C., Choudhuri, K., Chang, V.T., Lu, W., Davis, S.J., Van Der Merwe, P.A., Jones, E.Y.

(2007) Science 317: 1217

• PubMed: 17761881 
• DOI: 10.1126/science.1144646
• Primary Citation of Related Structures:  
  2V5Y


• PubMed Abstract: 
  

Cell-cell contacts are fundamental to multicellular organisms and are subject to exquisite levels of control. Human RPTPmu is a type IIB receptor protein tyrosine phosphatase that both forms an adhesive contact itself and is involved in regulating adhesion by dephosphorylating components of cadherin-catenin complexes. Here we describe a 3.1 angstrom crystal structure of the RPTPmu ectodomain that forms a homophilic trans (antiparallel) dimer with an extended and rigid architecture, matching the dimensions of adherens junctions. Cell surface expression of deletion constructs induces intercellular spacings that correlate with the ectodomain length. These data suggest that the RPTPmu ectodomain acts as a distance gauge and plays a key regulatory function, locking the phosphatase to its appropriate functional location.

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Organizational Affiliation: 

Cancer Research UK Receptor Structure Research Group, University of Oxford, Henry Wellcome Building of Genomic Medicine, Division of Structural Biology, Roosevelt Drive, Oxford OX3 7BN, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU	A	731	Homo sapiens	Mutation(s): 0  Gene Names: PTPRM, PTPRL1 EC: 3.1.3.48
Find proteins for P28827 (Homo sapiens) Explore P28827  Go to UniProtKB:  P28827
NIH Common Fund Data Resources
PHAROS:  P28827 GTEx:  ENSG00000173482

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	A	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 0.320 
• R-Value Work: 0.242 
• R-Value Observed: 0.246 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 167.336	α = 90
b = 69.325	β = 113.52
c = 97.487	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	phasing
PHASER	phasing
REFMAC	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-07-11 
• Released Date: 2007-09-11 
Deposition Author(s): Aricescu, A.R., Siebold, C., Choudhuri, K., Chang, V.T., Lu, W., Davis, S.J., van der Merwe, P.A., Jones, E.Y.

Revision History 

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary