9NXE: Calcineurin Clinical Variant E282K

Crystal Structure of Calcineurin Clinical Variant E282K. Determined by X-ray diffraction at 2.09 Å resolution. Released 17 Dec 2025.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Homo sapiens
Chains: 3
Atoms: 4,470
Mol. weight: 66.07 kDa
Ligands: FE, ZN, CA
Released: 17 Dec 2025

Explore 9NXE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9NXE contains 29 α-helices and 29 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 19 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	22-25	4
β-strand	28-29	2	1
α-helix	31-34	4
β-strand	35	1	2
β-strand	41	1	2
α-helix	43-51	9
β-strand	55-56	2	1
α-helix	58-73	16
β-strand	78-81	4	3
α-helix	82	1
β-strand	85-88	4	4
β-strand	90	1	5
α-helix	95-105	11
β-strand	113-115	3	4
α-helix	126-139	14
β-strand	144-146	3	4
α-helix	154-159	6
α-helix	162-169	8
α-helix	172-183	12
β-strand	188-191	4	3
β-strand	195-197	3	3
β-strand	203	1	6
β-strand	206	1	6
α-helix	209-213	5
α-helix	220-222	3
α-helix	226-232	7
β-strand	234-235	2	7
β-strand	248-250	3	7
β-strand	258-260	3	7
α-helix	262-271	10
β-strand	276-279	4	3
β-strand	288-290	3	3
α-helix	291-292	2
β-strand	293	1	8
α-helix	294	1
β-strand	300	1	8
β-strand	302-305	4	3
β-strand	306	1	5
α-helix	311-313	3
β-strand	319-325	7	4
β-strand	328-334	7	4
α-helix	344-346	3
α-helix	349-369	21

Chain B: 9 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	17-30	14
β-strand	37-38	2	9
α-helix	40-44	5
α-helix	47-49	3
α-helix	55-62	8
β-strand	70-71	2	9
α-helix	72-80	9
α-helix	88-99	12
β-strand	106-107	2	10
α-helix	109-120	12
α-helix	126-140	15
β-strand	148-149	2	10
α-helix	150-156	7

Chain C: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
α-helix	713-715	3
β-strand	716-720	5	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein phosphatase 3 catalytic subunit alpha	A	protein	370	Homo sapiens	Q08209 (AlphaFold model)
Calcineurin subunit B type 1	B	protein	156	Homo sapiens	P63098 (AlphaFold model)
Sodium/hydrogen exchanger 1	C	protein	48	Homo sapiens	P19634 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9NXE_1 Protein phosphatase 3 catalytic subunit alpha (chains A)
MSEPKAIDPKLSTTDRVVKAVPFPPSHRLTAKEVFDNDGKPRVDILKAHLMKEGRLEESV
ALRIITEGASILRQEKNLLDIDAPVTVCGDIHGQFFDLMKLFEVGGSPANTRYLFLGDYV
DRGYFSIECVLYLWALKILYPKTLFLLRGNHECRHLTEYFTFKQECKIKYSERVYDACMD
AFDCLPLAALMNQQFLCVHGGLSPEINTLDDIRKLDRFKEPPAYGPMCDILWSDPLEDFG
NEKTQEHFTHNTVRGCSYFYSYPAVCEFLQHNNLLSILRAHKAQDAGYRMYRKSQTTGFP
SLITIFSAPNYLDVYNNKAAVLKYENNVMNIRQFNCSPHPYWLPNFMDVFTWSLPFVGEK
VTEMLVNVLN

Sequence of entity 2 (B), FASTA

>9NXE_2 Calcineurin subunit B type 1 (chains B)
MDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKE
FIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVD
KTIINADKDGDGRISFEEFCAVVGGLDIHKKMVVDV

Sequence of entity 3 (C), FASTA

>9NXE_3 Sodium/hydrogen exchanger 1 (chains C)
GHMKINNYLTVPAHKLDSPTMSRARIGSDPLAYEPKEDLPVITIDPAS

Ligands and cofactors

ID	Name	Formula	Copies
FE	FE (III) ion	Fe	1
ZN	Zinc ion	Zn	1
CA	Calcium ion	Ca	4

Water and common crystallization additives (PEG) are not listed.

Primary citation

The clinical missense variant E282K in PPP3CA/calcineurin shifts substrate dephosphorylation by altering active site recruitment. Shirakawa, K.T., Parikh, T., Machado, L.E.S.F. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-69535-5 · PubMed

Other PDB entries of the same protein (UniProt Q08209 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2W73 1.45 Å, High-resolution structure of the complex between calmodulin and a peptide from…
4F0Z 1.7 Å, Crystal Structure of Calcineurin in Complex with the Calcineurin-Inhibiting Domain of…
6UUQ 1.85 Å, Structure of Calcineurin bound to RCAN1
2R28 1.86 Å, The complex Structure of Calmodulin Bound to a Calcineurin Peptide
6NUC 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
6NUF 1.9 Å, Structure of Calcineurin in complex with NHE1 peptide
4Q5U 1.95 Å, Structure of calmodulin bound to its recognition site from calcineurin
3LL8 2.0 Å, Crystal Structure of Calcineurin in Complex with AKAP79 Peptide
1AUI 2.1 Å, Human calcineurin heterodimer
9NXN 2.1 Å, Crystal structure of CN:RII alpha
2P6B 2.3 Å, Crystal Structure of Human Calcineurin in Complex with PVIVIT Peptide
6NUU 2.3 Å, Structure of Calcineurin mutant in complex with NHE1 peptide

Browse structure collections

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