9C7T | pdb_00009c7t

PP2A:B55-Eya3 substrate complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Cryo-EM structures of PP2A:B55 with p107 and Eya3 define substrate recruitment.

Padi, S.K.R.Godek, R.J.Peti, W.Page, R.

(2025) Nat Struct Mol Biol 32: 1373-1382

  • DOI: https://doi.org/10.1038/s41594-025-01535-3
  • Primary Citation of Related Structures:  
    9C6B, 9C7T

  • PubMed Abstract: 

    Phosphoprotein phosphatases (PPPs) achieve specificity by binding substrates and regulators using PPP-specific short motifs. Protein phosphatase 2A (PP2A) is a highly conserved phosphatase that regulates cell signaling and is a tumor suppressor. Here, we use cryo-electron microscopy and nuclear magnetic resonance (NMR) spectroscopy to investigate the mechanisms of human p107 substrate and Eya3 regulator recruitment to the PP2A:B55 holoenzyme. We show that, while they associate with B55 using a common set of interaction pockets, the mechanism of substrate and regulator binding differs and is distinct from that observed for PP2A:B56 and other PPPs. We also identify the core B55 recruitment motif in Eya3 proteins, a sequence conserved amongst the Eya family. Lastly, using NMR-based dephosphorylation assays, we demonstrate how B55 recruitment directs PP2A:B55 fidelity through the selective dephosphorylation of specific phosphosites. As PP2A:B55 orchestrates mitosis and DNA damage repair, these data provide a roadmap for pursuing new avenues to therapeutically target this complex by individually blocking a subset of regulators that use different B55 interaction sites.


  • Organizational Affiliation
    • Department of Molecular Biology and Biophysics, University of Connecticut Health Center, Farmington, CT, USA.

Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform584Homo 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 
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30153
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform451Homo sapiensMutation(s): 0 
Gene Names: PPP2R2A
UniProt & NIH Common Fund Data Resources
Find proteins for P63151 (Homo sapiens)
Explore P63151 
Go to UniProtKB:  P63151
PHAROS:  P63151
GTEx:  ENSG00000221914 
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UniProt GroupP63151
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform311Homo 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 
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UniProt GroupP67775
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Eyes absent homolog 352Homo sapiensMutation(s): 0 
Gene Names: EYA3
EC: 3.1.3.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q99504 (Homo sapiens)
Explore Q99504 
Go to UniProtKB:  Q99504
PHAROS:  Q99504
GTEx:  ENSG00000158161 
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UniProt GroupQ99504
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLL
Query on MLL
C
L-PEPTIDE LINKINGC7 H15 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC
MODEL REFINEMENTPHENIX

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM144379
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM144483

Revision History  (Full details and data files)

  • Version 1.0: 2025-05-21
    Type: Initial release
  • Version 1.1: 2025-08-20
    Changes: Data collection, Database references