3PS5 | pdb_00003ps5

Crystal structure of the full-length Human Protein Tyrosine Phosphatase SHP-1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 
    0.276 (Depositor), 0.268 (DCC) 
  • R-Value Work: 
    0.225 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 
    0.227 (Depositor) 

Starting Model: experimental
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This is version 1.3 of the entry. See complete history

Literature

Crystal structure of human protein tyrosine phosphatase SHP-1 in the open conformation.

Wang, W.Liu, L.Song, X.Mo, Y.Komma, C.Bellamy, H.D.Zhao, Z.J.Zhou, G.W.

(2011) J Cell Biochem 112: 2062-2071

  • DOI: https://doi.org/10.1002/jcb.23125
  • Primary Citation Related Structures: 
    3PS5

  • PubMed Abstract: 

    SHP-1 belongs to the family of non-receptor protein tyrosine phosphatases (PTPs) and generally acts as a negative regulator in a variety of cellular signaling pathways. Previously, the crystal structures of the tail-truncated SHP-1 and SHP-2 revealed an autoinhibitory conformation. To understand the regulatory mechanism of SHP-1, we have determined the crystal structure of the full-length SHP-1 at 3.1 Å. Although the tail was disordered in current structure, the huge conformational rearrangement of the N-SH2 domain and the incorporation of sulfate ions into the ligand-binding site of each domain indicate that the SHP-1 is in the open conformation. The N-SH2 domain in current structure is shifted away from the active site of the PTP domain to the other side of the C-SH2 domain, resulting in exposure of the active site. Meanwhile, the C-SH2 domain is twisted anticlockwise by about 110°. In addition, a set of new interactions between two SH2 domains and between the N-SH2 and the catalytic domains is identified, which could be responsible for the stabilization of SHP-1 in the open conformation. Based on the structural comparison, a model for the activation of SHP-1 is proposed.


  • Organizational Affiliation
    • Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA.

Macromolecule Content 

  • Total Structure Weight: 68.12 kDa 
  • Atom Count: 4,266 
  • Modeled Residue Count: 529 
  • Deposited Residue Count: 595 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Tyrosine-protein phosphatase non-receptor type 6595Homo sapiensMutation(s): 1 
Gene Names: PTPN6HCPPTP1C
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P29350 (Homo sapiens)
Explore P29350 
Go to UniProtKB:  P29350
PHAROS:  P29350
GTEx:  ENSG00000111679 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP29350
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free:  0.276 (Depositor), 0.268 (DCC) 
  • R-Value Work:  0.225 (Depositor), 0.218 (DCC) 
  • R-Value Observed: 0.227 (Depositor) 
Space Group: H 3 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 231.919α = 90
b = 231.919β = 90
c = 78.852γ = 120
Software Package:
Software NamePurpose
MAR345dtbdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-04-20
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-08-24
    Changes: Database references
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Derived calculations, Refinement description