9MIP | pdb_00009mip

CryoEM structure of the Protein Phasphatase 2A (Aalpha-B56gamma-Calpha) holoenzyme complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

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This is version 1.2 of the entry. See complete history

Literature

Regulatory mechanisms of PP2A complex assembly driven by physicochemical differences in A-subunit isoforms.

Day, A.Huang, W.Leonard, D.O'Connor, C.M.Narla, G.Taylor, D.J.

(2025) Structure 33: 1688-1699.e5

  • DOI: https://doi.org/10.1016/j.str.2025.06.013
  • Primary Citation Related Structures: 
    9MF5, 9MIP

  • PubMed Abstract: 

    Protein phosphatase 2A (PP2A) is crucial for regulating cellular pathways, with its holoenzyme assembly affecting enzyme function and substrate selection. The PP2A holoenzyme comprises scaffold A-, regulatory B-, and catalytic C-subunits, each with various isoforms. Here, we examine structural and biochemical characteristics of the A-subunit isoforms (Aα and Aβ) and identify different biophysical properties that may promote distinct PP2A functions. Our molecular dynamics simulations and cryo-EM analyses define structural differences in the isoforms that reside primarily at the N-terminus of the A-subunit where it interfaces with regulatory B-subunits. Kinetic analyses show Aβ has a lower binding affinity in complexes with B56 subunits and exhibits unique aggregative properties as a monomeric protein. These findings suggest that the different physicochemical properties between A-subunit isoforms are key to PP2A holoenzyme assembly and function. We predict that the Aβ serves as a reservoir, ensuring that serine-threonine phosphatase activity is maintained during high regulatory demand.


  • Organizational Affiliation
    • Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.

Macromolecule Content 

  • Total Structure Weight: 162.27 kDa 
  • Atom Count: 10,549 
  • Modeled Residue Count: 1,312 
  • Deposited Residue Count: 1,422 
  • Unique protein chains: 3

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform589Homo 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
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform524Homo sapiensMutation(s): 0 
Gene Names: PPP2R5CKIAA0044
UniProt & NIH Common Fund Data Resources
Find proteins for Q13362 (Homo sapiens)
Explore Q13362 
Go to UniProtKB:  Q13362
PHAROS:  Q13362
GTEx:  ENSG00000078304 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13362
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 3
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform309Homo sapiensMutation(s): 0 
Gene Names: PPP2CA
EC: 3.1.3.16
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

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.40 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1-4487

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United States--

Revision History  (Full details and data files)

  • Version 1.0: 2025-07-09
    Type: Initial release
  • Version 1.1: 2025-08-13
    Changes: Data collection, Database references
  • Version 1.2: 2025-10-15
    Changes: Data collection, Database references