9N0Y: PP2A-B55 Holoenzyme with Eya3

PP2A-B55 Holoenzyme with Eya3. Determined by electron microscopy at 3.71 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.71 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,792
Mol. weight: 215.41 kDa
Released: 18 Jun 2025

Explore 9N0Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N0Y contains 79 α-helices and 52 β-strands across 4 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: 57 helices, 0 β-strands

Element	Residues	Length
α-helix	11-20	10
α-helix	25-32	8
α-helix	35-42	8
α-helix	44-46	3
α-helix	47-51	5
α-helix	52-56	5
α-helix	63-74	12
α-helix	86-88	3
α-helix	90-96	7
α-helix	102-116	15
α-helix	121-123	3
α-helix	124-128	5
α-helix	129-135	7
α-helix	141-147	7
α-helix	151-154	4
α-helix	160-173	14
α-helix	179-195	17
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-213	8
α-helix	221-232	12
α-helix	240-244	5
α-helix	245-251	7
α-helix	257-264	8
α-helix	267-278	12
α-helix	279-283	5
α-helix	284-291	8
α-helix	296-304	9
α-helix	306-310	5
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-333	7
α-helix	339-346	8
α-helix	349-352	4
α-helix	353-360	8
α-helix	361-365	5
α-helix	366-372	7
α-helix	378-386	9
α-helix	389-395	7
α-helix	398-411	14
α-helix	417-434	18
α-helix	436-438	3
α-helix	439-443	5
α-helix	444-451	8
α-helix	456-473	18
α-helix	475-481	7
α-helix	483-489	7
α-helix	495-509	15
α-helix	514-516	3
α-helix	517-521	5
α-helix	522-528	7
α-helix	534-547	14
α-helix	548-550	3
α-helix	553-555	3
α-helix	556-560	5
α-helix	561-567	7
α-helix	574-585	12

Chain B: 8 helices, 36 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	1
α-helix	27-29	3
β-strand	34-36	3	2
β-strand	43-46	4	2
α-helix	48-50	3
β-strand	51-57	7	2
α-helix	68-70	3
β-strand	71-78	8	2
β-strand	100	1	3
β-strand	111-114	4	3
β-strand	118-122	5	3
β-strand	124-132	9	4
β-strand	137	1	5
β-strand	143	1	5
β-strand	156-166	11	4
β-strand	170-173	4	3
β-strand	183-185	3	6
β-strand	191-194	4	6
β-strand	199-200	2	7
β-strand	201-204	4	6
β-strand	207	1	6
β-strand	210-211	2	8
β-strand	215-216	2	7
β-strand	251-252	2	9
β-strand	268-269	2	9
α-helix	282-285	4
β-strand	291-293	3	10
β-strand	300-302	3	10
β-strand	310	1	10
α-helix	327-329	3
α-helix	333-337	5
β-strand	348-349	2	11
β-strand	356	1	12
β-strand	358-360	3	11
β-strand	366-369	4	11
β-strand	370	1	12
β-strand	376-378	3	11
β-strand	397-398	2	13
β-strand	408-409	2	13
α-helix	410-412	3
β-strand	434	1	14
β-strand	439	1	14
α-helix	442	1
β-strand	443-444	2	1

Chain C: 13 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	2-17	16
α-helix	25-39	15
β-strand	47	1	15
α-helix	48-49	2
β-strand	52-53	2	16
β-strand	54	1	17
α-helix	62-71	10
β-strand	80-82	3	17
α-helix	93-106	14
β-strand	111-113	3	17
α-helix	121-126	6
α-helix	129-137	9
α-helix	141-150	10
β-strand	157-159	3	15
β-strand	163-165	3	15
α-helix	177-182	6
α-helix	194-200	7
β-strand	210-211	2	18
β-strand	218-219	2	18
α-helix	222-231	10
β-strand	236-239	4	15
β-strand	248-251	4	15
β-strand	256-259	4	15
α-helix	265-267	3
β-strand	273	1	19
β-strand	277-278	2	16
β-strand	289	1	19
α-helix	291-293	3
β-strand	299-300	2	8

Chain D: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	78-80	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	A	protein	584	Homo sapiens	P30153 (AlphaFold model)
Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform	B	protein	451	Homo sapiens	P63151 (AlphaFold model)
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	C	protein	309	Homo sapiens	P67775 (AlphaFold model)
Protein phosphatase EYA3	D	protein	573	Homo sapiens	Q99504 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9N0Y_1 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (chains A)
GHMSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEV
LLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLE
AHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAA
ASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVM
PTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHK
VKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHL
LPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIE
YMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPK
VLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQ
KIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

Sequence of entity 2 (B), FASTA

>9N0Y_2 Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (chains B)
GHMGSAGAGGGNDIQWCFSQVKGAVDDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQ
QEQENKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTND
KTIKLWKISERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAH
TYHINSISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHP
NSCNTFVYSSSKGTIRLCDMRASALCDRHSKLFEEPEDPSNRSFFSEIISSISDVKFSHS
GRYMMTRDYLSVKIWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSV
VMTGSYNNFFRMFDRNTKRDITLEASRENNKPRTVLKPRKVCASGKRKKDEISVDSLDFN
KKILHTAWHPKENIIAVATTNNLYIFQDKVN

Sequence of entity 3 (C), FASTA

>9N0Y_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (chains C)
MDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHG
QFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHES
RQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHI
RALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRA
HQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHV
TRRTPDYFL

Sequence of entity 4 (D), FASTA

>9N0Y_4 Protein phosphatase EYA3 (chains D)
MEEEQDLPEQPVKKAKMQESGEQTISQVSNPDVSDQKPETSSLASNLPMSEEIMTCTDYI
PRSSNDYTSQMYSAKPYAHILSVPVSETAYPGQTQYQTLQQTQPYAVYPQATQTYGLPPF
GALWPGMKPESGLIQTPSPSQHSVLTCTTGLTTSQPSPAHYSYPIQASSTNASLISTSST
IANIPAAAVASISNQDYPTYTILGQNQYQACYPSSSFGVTGQTNSDAESTTLAATTYQSE
KPSVMAPAPAAQRLSSGDPSTSPSLSQTTPSKDTDDQSRKNMTSKNRGKRKADATSSQDS
ELERVFLWDLDETIIIFHSLLTGSYAQKYGKDPTVVIGSGLTMEEMIFEVADTHLFFNDL
EECDQVHVEDVASDDNGQDLSNYSFSTDGFSGSGGSGSHGSSVGVQGGVDWMRKLAFRYR
KVREIYDKHKSNVGGLLSPQRKEALQRLRAEIEVLTDSWLGTALKSLLLIQSRKNCVNVL
ITTTQLVPALAKVLLYGLGEIFPIENIYSATKIGKESCFERIVSRFGKKVTYVVIGDGRD
EEIAAKQHNMPFWRITNHGDLVSLHQALELDFL

Primary citation

Cryo-EM structures reveal the PP2A-B55 alpha and Eya3 interaction that can be disrupted by a peptide inhibitor. Shi, S., Li, X., Alderman, C. et al. J Biol Chem (2025) 301:110287-110287. DOI 10.1016/j.jbc.2025.110287 · PubMed

Other PDB entries of the same protein (UniProt P30153 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1B3U 2.3 Å, Crystal structure of constant regulatory domain of human PP2A, PR65ALPHA
4I5L 2.43 Å, Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6…
8TWE 2.55 Å, Cryo-EM structure of the PP2A:B55-FAM122A complex, B55 body
2IE4 2.6 Å, Structure of the Protein Phosphatase 2A Core Enzyme Bound to okadaic acid
9C6B 2.6 Å, PP2A:B55-p107 substrate complex
8TWI 2.69 Å, Cryo-EM structure of the PP2A:B55-FAM122A complex, PP2Ac body
8U1X 2.7 Å, The structure of the PP2A-B56Delta holoenzyme mutant - E197K
9C7T 2.7 Å, PP2A:B55-Eya3 substrate complex
8TTB 2.77 Å, Cryo-EM structure of the PP2A:B55-ARPP19 complex
8SO0 2.8 Å, Cryo-EM structure of the PP2A:B55-FAM122A complex
2IE3 2.8 Å, Structure of the Protein Phosphatase 2A Core Enzyme Bound to Tumor-inducing Toxins
3C5W 2.8 Å, Complex between PP2A-specific methylesterase PME-1 and PP2A core enzyme

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