4G9J | pdb_00004g9j

Protein Ser/Thr phosphatase-1 in complex with cell-permeable peptide

• PDB DOI: https://doi.org/10.2210/pdb4G9J/pdb

• Classification: HYDROLASE/HYDROLASE ACTIVATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21
• Mutation(s): No 


• Deposited: 2012-07-24 Released: 2012-09-19 
• Deposition Author(s): Sukackaite, R., Chatterjee, J., Beullens, M., Bollen, M., Koehn, M., Hart, D.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free: 
  0.276 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.224 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Development of a Peptide that Selectively Activates Protein Phosphatase-1 in Living Cells.

Chatterjee, J., Beullens, M., Sukackaite, R., Qian, J., Lesage, B., Hart, D.J., Bollen, M., Kohn, M.

(2012) Angew Chem Int Ed Engl 51: 10054-10059

• PubMed: 22962028 
• DOI: https://doi.org/10.1002/anie.201204308
• Primary Citation of Related Structures:  
  4G9J


• PubMed Abstract: 
  

  that activates protein phosphatase-1 (PP1) by disrupting a subset of PP1 complexes in living cells has been developed. Activated PP1 rapidly dephosphorylates its substrates, counteracting kinase activity inside cells. Activation of PP1 can thus be a novel approach to study PP1 function and to counteract Ser/Thr kinase activity under pathologically increased kinase signaling.

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Organizational Affiliation: 

Genome Biology Unit, EMBL, Meyerhofstrasse 1, 69117 Heidelberg, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 80.95 kDa 
• Atom Count: 4,944 
• Modelled Residue Count: 612 
• Deposited Residue Count: 708 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase PP1-alpha catalytic subunit	A, B	331	Homo sapiens	Mutation(s): 0  Gene Names: PPP1A, PPP1CA 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
synthetic peptide	C, D	23	N/A	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	E [auth A], F [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.10 Å
• R-Value Free:  0.276 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.224 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 4₂ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 138.007	α = 90
b = 138.007	β = 90
c = 113.675	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MxCuBE	data collection
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-09-19 
Deposition Author(s): Sukackaite, R., Chatterjee, J., Beullens, M., Bollen, M., Koehn, M., Hart, D.J.

Revision History  

• Version 1.0: 2012-09-19
  Type: Initial release
  
• Version 1.1: 2012-10-10
  Changes: Database references
• Version 1.2: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description