8UWB

Crystal structure of PP2A PPP2R1A-PPP2CA-PPP2R5E phosphatase.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


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Literature

Structural characterization of methylation-independent PP2A assembly guides Alphafold2Multimer prediction of family-wide PP2A complexes.

Wachter, F.Nowak, R.P.Ficarro, S.Marto, J.Fischer, E.S.

(2024) J Biol Chem : 107268-107268

  • DOI: https://doi.org/10.1016/j.jbc.2024.107268
  • Primary Citation of Related Structures:  
    8UWB

  • PubMed Abstract: 

    Dysregulation of phosphorylation-dependent signaling is a hallmark of tumorigenesis. Protein phosphatase 2 (PP2A) is an essential regulator of cell growth. One scaffold subunit (A) binds to a catalytic subunit (C) to form a core AC heterodimer, which together with one of many regulatory (B) subunits forms the active trimeric enzyme. The combinatorial number of distinct PP2A complexes is large, which results in diverse substrate specificity and subcellular localization. The detailed mechanism of PP2A assembly and regulation remains elusive and reports about an important role of methylation of the carboxy terminus of PP2A C are conflicting. A better understanding of the molecular underpinnings of PP2A assembly and regulation is critical to dissect PP2A function in physiology and disease. Here, we combined biochemical reconstitution, mass spectrometry, X-ray crystallography and functional assays to characterize the assembly of trimeric PP2A. In vitro studies demonstrated that methylation of the carboxy-terminus of PP2A C was dispensable for PP2A assembly in vitro. To corroborate these findings, we determined the X-ray crystal structure of the unmethylated PP2A Aα-B56ε-Cα trimer complex to 3.1 Å resolution. The experimental structure superimposed well with an Alphafold2Multimer prediction of the PP2A trimer. We then predicted models of all canonical PP2A complexes providing a framework for structural analysis of PP2A. In conclusion, methylation was dispensable for trimeric PP2A assembly and integrative structural biology studies of PP2A offered predictive models for all canonical PP2A complexes.


  • Organizational Affiliation

    Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
A, D
612Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
UniProt & NIH Common Fund Data Resources
Find proteins for P67775 (Homo sapiens)
Explore P67775 
Go to UniProtKB:  P67775
PHAROS:  P67775
GTEx:  ENSG00000113575 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP67775
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit epsilon isoform
B, E
467Homo sapiensMutation(s): 0 
Gene Names: PPP2R5E
UniProt & NIH Common Fund Data Resources
Find proteins for Q16537 (Homo sapiens)
Explore Q16537 
Go to UniProtKB:  Q16537
PHAROS:  Q16537
GTEx:  ENSG00000154001 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16537
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
C, F
333Homo sapiensMutation(s): 0 
Gene Names: PPP2R1A
UniProt & NIH Common Fund Data Resources
Find proteins for P30153 (Homo sapiens)
Explore P30153 
Go to UniProtKB:  P30153
PHAROS:  P30153
GTEx:  ENSG00000105568 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30153
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.263 
  • R-Value Work: 0.221 
  • R-Value Observed: 0.223 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.839α = 83.77
b = 92.597β = 72.46
c = 134.657γ = 73.46
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
pointlessdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Other privateUnited StatesASH Scholar Award
Other privateClaudia Adams Barr Award
Other privateWipe Out Kids Cancer
Other privatePedals for Pediatrics
Other privateBCH Faculty Development Award
The Mark FoundationUnited StatesMark Foundation Emerging Leaders Award

Revision History  (Full details and data files)

  • Version 1.0: 2024-04-17
    Type: Initial release