Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 293.25 kDa 
• Atom Count: 20212 
• Residue Count: 2540 
• Unique protein chains: 4

2NYL

Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated

• DOI: 10.2210/pdb2NYL/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Cyanobacteria
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2006-11-20 Released: 2006-12-12 
• Deposition Author(s): Xing, Y., Xu, Y., Chen, Y., Chao, Y., Lin, Z., Shi, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.335 
• R-Value Work: 0.282 
• R-Value Observed: 0.300 

Literature

Structure of the Protein Phosphatase 2A Holoenzyme.

Xu, Y., Xing, Y., Chen, Y., Chao, Y., Lin, Z., Fan, E., Yu, J.W., Strack, S., Jeffrey, P.D., Shi, Y.

(2006) Cell 127: 1239-1251

• PubMed: 17174897 
• DOI: 10.1016/j.cell.2006.11.033
• Primary Citation of Related Structures:  
  2NYM, 2NYL, 2NPP


• PubMed Abstract: 
  

Protein Phosphatase 2A (PP2A) plays an essential role in many aspects of cellular physiology. The PP2A holoenzyme consists of a heterodimeric core enzyme, which comprises a scaffolding subunit and a catalytic subunit, and a variable regulatory subunit. Here we report the crystal structure of the heterotrimeric PP2A holoenzyme involving the regulatory subunit B'/B56/PR61. Surprisingly, the B'/PR61 subunit has a HEAT-like (huntingtin-elongation-A subunit-TOR-like) repeat structure, similar to that of the scaffolding subunit. The regulatory B'/B56/PR61 subunit simultaneously interacts with the catalytic subunit as well as the conserved ridge of the scaffolding subunit. The carboxyterminus of the catalytic subunit recognizes a surface groove at the interface between the B'/B56/PR61 subunit and the scaffolding subunit. Compared to the scaffolding subunit in the PP2A core enzyme, formation of the holoenzyme forces the scaffolding subunit to undergo pronounced conformational rearrangements. This structure reveals significant ramifications for understanding the function and regulation of PP2A.

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Organizational Affiliation: 

Department of Molecular Biology, Lewis Thomas Laboratory, Princeton University, Princeton, NJ 08544, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform	A, D	582	Homo sapiens	Mutation(s): 0  Gene Names: PPP2R1A
Find proteins for P30153 (Homo sapiens) Explore P30153  Go to UniProtKB:  P30153
NIH Common Fund Data Resources
PHAROS  P30153 GTEx  ENSG00000105568

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform	B, E	388	Homo sapiens	Mutation(s): 0  Gene Names: PPP2R5C, KIAA0044
Find proteins for Q13362 (Homo sapiens) Explore Q13362  Go to UniProtKB:  Q13362
NIH Common Fund Data Resources
PHAROS  Q13362 GTEx  ENSG00000078304

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	C, F	293	Homo sapiens	Mutation(s): 0  Gene Names: PPP2CA EC: 3.1.3.16
Find proteins for P67775 (Homo sapiens) Explore P67775  Go to UniProtKB:  P67775
NIH Common Fund Data Resources
PHAROS  P67775 GTEx  ENSG00000113575

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
microcystin LR	G, H	7	Cyanobacteria	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MN	C, F	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A,D	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000212	G, H	Microcystin LR	Oligopeptide /  Toxin		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.80 Å
• R-Value Free: 0.335 
• R-Value Work: 0.282 
• R-Value Observed: 0.300 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.48	α = 90
b = 159.85	β = 90
c = 270.37	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-11-20 
• Released Date: 2006-12-12 
Deposition Author(s): Xing, Y., Xu, Y., Chen, Y., Chao, Y., Lin, Z., Shi, Y.

Revision History 

• Version 1.0: 2006-12-12
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2011-07-27
  Changes: Database references, Derived calculations, Non-polymer description
• Version 1.4: 2013-02-27
  Changes: Other
• Version 1.5: 2017-10-18
  Changes: Advisory, Refinement description