Biological Assembly 1  

 3D View: Structure

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 60.35 kDa 
• Atom Count: 4062 
• Residue Count: 504 
• Unique protein chains: 1

2B3O

Crystal structure of human tyrosine phosphatase SHP-1

• DOI: 10.2210/pdb2B3O/pdb

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


• Deposited: 2005-09-20 Released: 2005-10-25 
• Deposition Author(s): Yang, J., Liu, L., He, D., Song, X., Liang, X., Zhao, Z.J., Zhou, G.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.233 
• R-Value Observed: 0.241 

Literature

Crystal structure of human protein-tyrosine phosphatase SHP-1.

Yang, J., Liu, L., He, D., Song, X., Liang, X., Zhao, Z.J., Zhou, G.W.

(2003) J Biol Chem 278: 6516-6520

• PubMed: 12482860 
• DOI: 10.1074/jbc.M210430200
• Primary Citation of Related Structures:  
  2B3O


• PubMed Abstract: 
  

SHP-1 is a cytosolic protein-tyrosine phosphatase that behaves as a negative regulator in eukaryotic cellular signaling pathways. To understand its regulatory mechanism, we have determined the crystal structure of the C-terminal truncated human SHP-1 in the inactive conformation at 2.8-A resolution and refined the structure to a crystallographic R-factor of 24.0%. The three-dimensional structure shows that the ligand-free SHP-1 has an auto-inhibited conformation. Its N-SH2 domain blocks the catalytic domain and keeps the enzyme in the inactive conformation, which supports that the phosphatase activity of SHP-1 is primarily regulated by the N-SH2 domain. In addition, the C-SH2 domain of SHP-1 has a different orientation from and is more flexible than that of SHP-2, which enables us to propose an enzymatic activation mechanism in which the C-SH2 domains of SHPs could be involved in searching for phosphotyrosine activators.

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Organizational Affiliation: 

Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Tyrosine-protein phosphatase, non-receptor type 6	A	532	Homo sapiens	Mutation(s): 0  Gene Names: PTPN6, HCP, PTP1C EC: 3.1.3.48
Find proteins for P29350 (Homo sapiens) Explore P29350  Go to UniProtKB:  P29350
NIH Common Fund Data Resources
PHAROS  P29350 GTEx  ENSG00000111679

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.296 
• R-Value Work: 0.233 
• R-Value Observed: 0.241 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.736	α = 90
b = 100.404	β = 90
c = 149.475	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALA	data scaling
AMoRE	phasing
CNS	refinement
CCP4	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-09-20 
• Released Date: 2005-10-25 
Deposition Author(s): Yang, J., Liu, L., He, D., Song, X., Liang, X., Zhao, Z.J., Zhou, G.W.

Revision History 

• Version 1.0: 2005-10-25
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance