Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

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

Macromolecule Content

• Total Structure Weight: 30.64 kDa 
• Atom Count: 2208 
• Modelled Residue Count: 259 
• Deposited Residue Count: 259 
• Unique protein chains: 1

2C9A

Crystal structure of the MAM-Ig module of receptor protein tyrosine phosphatase mu

• PDB DOI: 10.2210/pdb2C9A/pdb

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


• Deposited: 2005-12-09 Released: 2006-01-19 
• Deposition Author(s): Aricescu, A.R., Hon, W.C., Siebold, C., Lu, W., Van Der Merwe, P.A., Jones, E.Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 

Literature

Molecular Analysis of Receptor Protein Tyrosine Phosphatase Mu-Mediated Cell Adhesion.

Aricescu, A.R., Hon, W.C., Siebold, C., Lu, W., Van Der Merwe, P.A., Jones, E.Y.

(2006) EMBO J 25: 701

• PubMed: 16456543 
• DOI: 10.1038/sj.emboj.7600974
• Primary Citation of Related Structures:  
  2C9A


• PubMed Abstract: 
  

Type IIB receptor protein tyrosine phosphatases (RPTPs) are bi-functional cell surface molecules. Their ectodomains mediate stable, homophilic, cell-adhesive interactions, whereas the intracellular catalytic regions can modulate the phosphorylation state of cadherin/catenin complexes. We describe a systematic investigation of the cell-adhesive properties of the extracellular region of RPTPmu, a prototypical type IIB RPTP. The crystal structure of a construct comprising its N-terminal MAM (meprin/A5/mu) and Ig domains was determined at 2.7 A resolution; this assigns the MAM fold to the jelly-roll family and reveals extensive interactions between the two domains, which form a rigid structural unit. Structure-based site-directed mutagenesis, serial domain deletions and cell-adhesion assays allowed us to identify the four N-terminal domains (MAM, Ig, fibronectin type III (FNIII)-1 and FNIII-2) as a minimal functional unit. Biophysical characterization revealed at least two independent types of homophilic interaction which, taken together, suggest that there is the potential for formation of a complex and possibly ordered array of receptor molecules at cell contact sites.

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Organizational Affiliation: 

Division of Structural Biology, Henry Wellcome Building of Genomic Medicine, University of Oxford, Oxford, UK.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE MU	A	259	Homo sapiens	Mutation(s): 0  Gene Names: PTPRM, PTPRL1 EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P28827 (Homo sapiens) Explore P28827  Go to UniProtKB:  P28827
PHAROS:  P28827 GTEx:  ENSG00000173482

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
alpha-D-mannopyranose-(1-3)-alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G48068RF GlyCosmos:  G48068RF GlyGen:  G48068RF

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

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

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 0.275 
• R-Value Work: 0.222 
• R-Value Observed: 0.225 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.856	α = 90
b = 97.737	β = 90
c = 134.357	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-12-09 
• Released Date: 2006-01-19 
Deposition Author(s): Aricescu, A.R., Hon, W.C., Siebold, C., Lu, W., Van Der Merwe, P.A., Jones, E.Y.

Revision History  

• Version 1.0: 2006-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 2.0: 2019-09-11
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Experimental preparation, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary