1YGR

Crystal structure of the tandem phosphatase domain of RPTP CD45

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 

wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history. 


Literature

Structural basis for the function and regulation of the receptor protein tyrosine phosphatase CD45.

Nam, H.J., Poy, F., Saito, H., Frederick, C.A.

(2005) J Exp Med 201: 441-452

  • DOI: 10.1084/jem.20041890
  • Primary Citation of Related Structures:  
    1YGR, 1YGU

  • PubMed Abstract: 

    • CD45 is the prototypic member of transmembrane receptor-like protein tyrosine phosphatases (RPTPs) and has essential roles in immune functions. The cytoplasmic region of CD45, like many other RPTPs, contains two homologous protein tyrosine phosphatase domains, active domain 1 (D1) and catalytically impaired domain 2 (D2) ...

    CD45 is the prototypic member of transmembrane receptor-like protein tyrosine phosphatases (RPTPs) and has essential roles in immune functions. The cytoplasmic region of CD45, like many other RPTPs, contains two homologous protein tyrosine phosphatase domains, active domain 1 (D1) and catalytically impaired domain 2 (D2). Here, we report crystal structure of the cytoplasmic D1D2 segment of human CD45 in native and phosphotyrosyl peptide-bound forms. The tertiary structures of D1 and D2 are very similar, but doubly phosphorylated CD3zeta immunoreceptor tyrosine-based activation motif peptide binds only the D1 active site. The D2 "active site" deviates from the other active sites significantly to the extent that excludes any possibility of catalytic activity. The relative orientation of D1 and D2 is very similar to that observed in leukocyte common antigen-related protein with both active sites in an open conformation and is restrained through an extensive network of hydrophobic interactions, hydrogen bonds, and salt bridges. This crystal structure is incompatible with the wedge model previously suggested for CD45 regulation.

    Organizational Affiliation: 

    Dana-Farber Cancer Institute, Boston, MA 02115, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CD45 Protein Tyrosine PhosphataseA, B610Homo sapiensMutation(s): 16 
Gene Names: PTPRC, CD45
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for P08575 (Homo sapiens)
Explore P08575 
Go to UniProtKB:  P08575
PHAROS:  P08575
GTEx:  ENSG00000081237 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08575
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
T-cell Receptor CD3 zeta ITAM-1C, D6N/AMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P20963 (Homo sapiens)
Explore P20963 
Go to UniProtKB:  P20963
PHAROS:  P20963
GTEx:  ENSG00000198821 
Entity Groups  
UniProt GroupP20963
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE		A, B L-PEPTIDE LINKINGC5 H11 N O2 SeMET
PTR
Query on PTR		C, D L-PEPTIDE LINKINGC9 H12 N O6 PTYR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.312 
  • R-Value Work: 0.255 
  • R-Value Observed: 0.255 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.01α = 90
b = 59.7β = 99.53
c = 160.53γ = 90
Software Package:
Software NamePurpose
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-02-22
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2018-04-18
    Changes: Data collection
  • Version 1.4: 2021-10-20
    Changes: Database references, Derived calculations