9NXN | pdb_00009nxn

Crystal structure of CN:RII alpha

• PDB DOI: https://doi.org/10.2210/pdb9NXN/pdb

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


• Deposited: 2025-03-25 Released: 2025-12-17 
• Deposition Author(s): Shirakawa, K.T., Parikh, T., Page, R., Peti, W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.211 (Depositor) 

Starting Model: experimental

Literature

CN:Tak1 complex explains CN substrate specificity

Shirakawa, K.T., Parikh, T., Page, R., Peti, W.

To be published.

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 69.05 kDa 
• Atom Count: 4,670 
• Modeled Residue Count: 527 
• Deposited Residue Count: 604 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Serine/threonine-protein phosphatase 2B catalytic subunit alpha isoform	A	370	Homo sapiens	Mutation(s): 0  Gene Names: PPP3CA, CALNA, CNA EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for Q08209 (Homo sapiens) Explore Q08209  Go to UniProtKB:  Q08209
PHAROS:  Q08209 GTEx:  ENSG00000138814

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Calcineurin subunit B type 1	B	170	Homo sapiens	Mutation(s): 0  Gene Names: PPP3R1, CNA2, CNB
UniProt & NIH Common Fund Data Resources
Find proteins for P63098 (Homo sapiens) Explore P63098  Go to UniProtKB:  P63098
PHAROS:  P63098 GTEx:  ENSG00000221823

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
cAMP-dependent protein kinase type II-alpha regulatory subunit	C	64	Homo sapiens	Mutation(s): 0  Gene Names: PRKAR2A, PKR2, PRKAR2
UniProt & NIH Common Fund Data Resources
Find proteins for P13861 (Homo sapiens) Explore P13861  Go to UniProtKB:  P13861
PHAROS:  P13861 GTEx:  ENSG00000114302

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	D [auth B], E [auth B], F [auth B], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.250 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.209 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.211 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.535	α = 90
b = 102.982	β = 90
c = 107.987	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROTEUM PLUS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2025-12-17 
Deposition Author(s): Shirakawa, K.T., Parikh, T., Page, R., Peti, W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01GM144379
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01NS124666

Revision History  

• Version 1.0: 2025-12-17
  Type: Initial release