4NY3 | pdb_00004ny3

Human PTPA in complex with peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.185 (Depositor), 0.187 (DCC) 
  • R-Value Work: 
    0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 
    0.159 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4NY3

This is version 1.1 of the entry. See complete history

Literature

Structural basis for PTPA interaction with the invariant C-terminal tail of PP2A.

Low, C.Quistgaard, E.M.Kovermann, M.Anandapadamanaban, M.Balbach, J.Nordlund, P.

(2014) Biol Chem 395: 881-889

  • DOI: https://doi.org/10.1515/hsz-2014-0106
  • Primary Citation Related Structures: 
    4NY3

  • PubMed Abstract: 

    Protein phosphatase 2A (PP2A) is a highly abundant heterotrimeric Ser/Thr phosphatase involved in the regulation of a variety of signaling pathways. The PP2A phosphatase activator (PTPA) is an ATP-dependent activation chaperone, which plays a key role in the biogenesis of active PP2A. The C-terminal tail of the catalytic subunit of PP2A is highly conserved and can undergo a number of posttranslational modifications that serve to regulate the function of PP2A. Here we have studied structurally the interaction of PTPA with the conserved C-terminal tail of the catalytic subunit carrying different posttranslational modifications. We have identified an additional interaction site for the invariant C-terminal tail of the catalytic subunit on PTPA, which can be modulated via posttranslational modifications. We show that phosphorylation of Tyr307(PP2A-C) or carboxymethylation of Leu309(PP2A-C) abrogates or diminishes binding of the C-terminal tail, whereas phosphorylation of Thr304(PP2A-C) is of no consequence. We suggest that the invariant C-terminal residues of the catalytic subunit can act as affinity enhancer for different PP2A interaction partners, including PTPA, and a different 'code' of posttranslational modifications can favour interactions to one subunit over others.

Macromolecule Content 

  • Total Structure Weight: 72.55 kDa 
  • Atom Count: 5,761 
  • Modeled Residue Count: 607 
  • Deposited Residue Count: 620 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A activator
A, B
304Homo sapiensMutation(s): 0 
Gene Names: PPP2R4PTPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q15257 (Homo sapiens)
Explore Q15257 
Go to UniProtKB:  Q15257
PHAROS:  Q15257
GTEx:  ENSG00000119383 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15257
Sequence Annotations
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Reference Sequence
Find similar proteins by:  Sequence   |   3D Structure  
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
C, D
6Homo sapiensMutation(s): 0 
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
UniProt GroupP67775
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
K [auth B],
L [auth B],
M [auth B],
N [auth B],
O [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL



Download:Ideal Coordinates CCD File
J [auth A],
P [auth B],
Q [auth B],
R [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.185 (Depositor), 0.187 (DCC) 
  • R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
  • R-Value Observed: 0.159 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 43.67α = 84.41
b = 47.97β = 80.23
c = 87.18γ = 88.23
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-07-23
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations