3EGH

Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1), the PP1 binding and PDZ domains of Spinophilin and the small natural molecular toxin Nodularin-R

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


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


Literature

Spinophilin directs protein phosphatase 1 specificity by blocking substrate binding sites.

Ragusa, M.J., Dancheck, B., Critton, D.A., Nairn, A.C., Page, R., Peti, W.

(2010) Nat Struct Mol Biol 17: 459-464

  • DOI: 10.1038/nsmb.1786
  • Primary Citation of Related Structures:  
    3EGG, 3EGH, 3HVQ

  • PubMed Abstract: 

    • The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets. PP1 associates with >or=200 regulatory proteins to form highly specific holoenzymes. These regulatory proteins target PP1 to its point of action within the cell and prime its enzymatic specificity for particular substrates ...

    The serine/threonine protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets. PP1 associates with >or=200 regulatory proteins to form highly specific holoenzymes. These regulatory proteins target PP1 to its point of action within the cell and prime its enzymatic specificity for particular substrates. However, how they direct PP1's specificity is not understood. Here we show that spinophilin, a neuronal PP1 regulator, is entirely unstructured in its unbound form, and it binds PP1 through a folding-upon-binding mechanism in an elongated fashion, blocking one of PP1's three putative substrate binding sites without altering its active site. This mode of binding is sufficient for spinophilin to restrict PP1's activity toward a model substrate in vitro without affecting its ability to dephosphorylate its neuronal substrate, glutamate receptor 1 (GluR1). Thus, our work provides the molecular basis for the ability of spinophilin to dictate PP1 substrate specificity.

    Organizational Affiliation: 

    Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, Rhode Island, USA.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-alpha catalytic subunitA, B329Homo sapiensMutation(s): 0 
Gene Names: PPP1CA, PPP1A
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P62136 (Homo sapiens)
Explore P62136 
Go to UniProtKB:  P62136
PHAROS:  P62136
GTEx:  ENSG00000172531
Protein Feature View
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  • Reference Sequence
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
SpinophilinC, D170Rattus norvegicusMutation(s): 0 
Gene Names: Ppp1r9b, Spino
UniProt
Find proteins for O35274 (Rattus norvegicus)
Explore O35274 
Go to UniProtKB:  O35274
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
nodularin RE, F5Nodularia spumigenaMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000214
Query on PRD_000214		E, FNODULARIN-ROligopeptide /  Toxin Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 119.409α = 90
b = 84.426β = 93.58
c = 109.314γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
HKL-2000data scaling
REFMACphasing

Structure Validation

View Full Validation Report


View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
  • Version 1.2: 2012-12-12
    Changes: Other
  • Version 1.3: 2013-04-10
    Changes: Derived calculations
  • Version 1.4: 2017-10-25
    Changes: Advisory, Refinement description