9N0Z: PP2A-B55 Holoenzyme with B55i

PP2A-B55 Holoenzyme with B55i. Determined by electron microscopy at 3.5 Å resolution. Released 18 Jun 2025.

Method: Electron microscopy
Resolution: 3.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,847
Mol. weight: 157.12 kDa
Released: 18 Jun 2025

Explore 9N0Z in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9N0Z contains 74 α-helices and 65 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: 53 helices, 0 β-strands

Element	Residues	Length
α-helix	11-19	9
α-helix	25-42	18
α-helix	47-51	5
α-helix	52-55	4
α-helix	63-73	11
α-helix	86-88	3
α-helix	91-94	4
α-helix	103-116	14
α-helix	121-123	3
α-helix	124-128	5
α-helix	129-135	7
α-helix	143-147	5
α-helix	160-173	14
α-helix	179-193	15
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-213	8
α-helix	223-234	12
α-helix	245-252	8
α-helix	257-265	9
α-helix	267-274	8
α-helix	276-278	3
α-helix	279-283	5
α-helix	284-291	8
α-helix	297-304	8
α-helix	306-311	6
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-334	8
α-helix	339-348	10
α-helix	349-355	7
α-helix	359-360	2
α-helix	361-365	5
α-helix	366-374	9
α-helix	380-386	7
α-helix	389-392	4
α-helix	401-412	12
α-helix	417-434	18
α-helix	437-441	5
α-helix	444-451	8
α-helix	456-479	24
α-helix	482-488	7
α-helix	489-491	3
α-helix	495-512	18
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	573-585	13

Chain B: 3 helices, 46 β-strands

Element	Residues	Length	Sheet
β-strand	12-13	2	1
α-helix	27-29	3
β-strand	35-36	2	2
β-strand	43-44	2	2
β-strand	51-52	2	3
β-strand	54-57	4	2
β-strand	71-73	3	2
β-strand	77-78	2	3
β-strand	98	1	4
β-strand	101	1	4
β-strand	109-114	6	4
β-strand	119-125	7	4
β-strand	129-132	4	5
β-strand	137	1	6
β-strand	143	1	6
β-strand	156-159	4	5
β-strand	165-166	2	4
β-strand	170-172	3	4
β-strand	180	1	7
β-strand	184-185	2	8
β-strand	191-195	5	8
β-strand	196	1	7
β-strand	199-204	6	8
β-strand	207	1	8
β-strand	211-212	2	9
β-strand	213-216	4	8
β-strand	245	1	10
β-strand	251-252	2	10
β-strand	268-269	2	10
β-strand	291	1	11
β-strand	299	1	12
β-strand	302-303	2	11
β-strand	307-310	4	11
β-strand	312	1	12
β-strand	321-324	4	11
α-helix	327-329	3
α-helix	335-337	3
β-strand	348-350	3	13
β-strand	357-360	4	13
β-strand	365-368	4	13
β-strand	369	1	14
β-strand	376	1	14
β-strand	379-380	2	13
β-strand	398	1	15
β-strand	409	1	15
β-strand	421-424	4	16
β-strand	431-434	4	16
β-strand	440	1	16
β-strand	443-444	2	1

Chain C: 15 helices, 19 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	25-40	16
β-strand	45-48	4	17
α-helix	49	1
β-strand	52	1	18
β-strand	53	1	19
β-strand	57	1	20
α-helix	62-72	11
β-strand	80-81	2	19
α-helix	93-106	14
α-helix	108-110	3
β-strand	111-112	2	19
α-helix	121-126	6
α-helix	129-136	8
α-helix	141-152	12
β-strand	156-159	4	17
β-strand	163-166	4	17
α-helix	178-181	4
α-helix	194-200	7
β-strand	210	1	21
β-strand	219	1	21
α-helix	222-232	11
β-strand	237-239	3	17
β-strand	250-251	2	17
β-strand	256-258	3	17
β-strand	260	1	20
α-helix	265-267	3
β-strand	273	1	22
β-strand	276-278	3	18
β-strand	284-286	3	18
β-strand	289	1	22
α-helix	290	1
α-helix	292-294	3
β-strand	300-301	2	9

Chain D: 3 helices, 0 β-strands

Element	Residues	Length
α-helix	4-7	4
α-helix	9-12	4
α-helix	21-31	11

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	311	Homo sapiens	P67775 (AlphaFold model)
B55i inhibitor peptide	D	protein	35	Homo sapiens

Sequence of entity 1 (A), FASTA

>9N0Z_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

>9N0Z_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

>9N0Z_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (chains C)
GHMDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDV
HGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNH
ESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLD
HIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVS
RAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEP
HVTRRTPDYFL

Sequence of entity 4 (D), FASTA

>9N0Z_4 B55i inhibitor peptide (chains D)
LLELAKKKLKELEEEEPDPDLRKKTLVRNMIKKLE

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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