Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 293245.13 
• 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
• Expression System: Escherichia coli BL21(DE3), Spodoptera frugiperda


• 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: 3.8 Å
• R-Value Free: 0.335 
• R-Value Work: 0.282 

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, 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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: PPP2R1A Go to UniProtKB:  P30153

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: PPP2R5C Go to UniProtKB:  Q13362

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
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) Go to Gene View: PPP2CA Go to UniProtKB:  P67775

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
microcystin LR	G, H	7	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

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

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000212	G,H	Microcystin LR	Oligopeptide / Toxin		--

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.8 Å
• R-Value Free: 0.335 
• R-Value Work: 0.282 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 108.480	α = 90.00
b = 159.850	β = 90.00
c = 270.370	γ = 90.00

Software Package:

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

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
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2011-07-27
  Type: Database references, Derived calculations, Non-polymer description
• Version 1.4: 2013-02-27
  Type: Other
• Version 1.5: 2017-10-18
  Type: Advisory, Refinement description