9C6B: PP2A:B55-p107 substrate complex

PP2A:B55-p107 substrate complex. Determined by electron microscopy at 2.6 Å resolution. Released 21 May 2025.

Method: Electron microscopy
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 4
Atoms: 10,737
Mol. weight: 161.74 kDa
Ligands: ZN, FE2
Released: 21 May 2025

Explore 9C6B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9C6B contains 94 α-helices and 55 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: 63 helices, 0 β-strands

Element	Residues	Length
α-helix	11-19	9
α-helix	25-33	9
α-helix	35-42	8
α-helix	45-46	2
α-helix	47-51	5
α-helix	52-56	5
α-helix	63-73	11
α-helix	83-89	7
α-helix	90-96	7
α-helix	102-116	15
α-helix	121-123	3
α-helix	124-128	5
α-helix	129-136	8
α-helix	141-147	7
α-helix	148-150	3
α-helix	151-154	4
α-helix	155-157	3
α-helix	160-174	15
α-helix	179-193	15
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-213	8
α-helix	218-221	4
α-helix	224-232	9
α-helix	237-243	7
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	296-304	9
α-helix	306-311	6
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-334	8
α-helix	339-349	11
α-helix	353-356	4
α-helix	358-360	3
α-helix	361-365	5
α-helix	366-373	8
α-helix	378-386	9
α-helix	389-392	4
α-helix	398-412	15
α-helix	417-425	9
α-helix	427-434	8
α-helix	436-438	3
α-helix	439-443	5
α-helix	444-450	7
α-helix	456-473	18
α-helix	475-477	3
α-helix	478-482	5
α-helix	483-486	4
α-helix	487-491	5
α-helix	495-516	22
α-helix	517-521	5
α-helix	522-527	6
α-helix	528-530	3
α-helix	534-546	13
α-helix	553-555	3
α-helix	556-560	5
α-helix	561-567	7
α-helix	573-586	14

Chain B: 14 helices, 37 β-strands

Element	Residues	Length	Sheet
β-strand	12-18	7	1
β-strand	31-36	6	2
β-strand	42-47	6	2
β-strand	51-57	7	2
β-strand	71-78	8	2
β-strand	83-85	3	3
β-strand	90-92	3	3
α-helix	93	1
β-strand	98-101	4	4
α-helix	102-103	2
β-strand	109-114	6	4
β-strand	119-132	14	4
β-strand	137	1	5
α-helix	142	1
β-strand	143	1	5
α-helix	144-145	2
α-helix	146-148	3
β-strand	156-172	17	4
β-strand	182-185	4	6
β-strand	191-195	5	6
β-strand	199-204	6	6
β-strand	207-216	10	6
α-helix	222-224	3
β-strand	229-234	6	7
β-strand	241-246	6	7
β-strand	251-255	5	7
β-strand	267-269	3	7
α-helix	272-274	3
α-helix	275-277	3
β-strand	290-293	4	8
β-strand	299-303	5	8
β-strand	307-312	6	8
β-strand	321-324	4	8
α-helix	327-329	3
α-helix	333-338	6
α-helix	341-343	3
β-strand	348-350	3	9
β-strand	356-360	5	9
β-strand	362	1	10
β-strand	365-370	6	9
β-strand	376-380	5	9
α-helix	383-385	3
β-strand	390-391	2	1
α-helix	392-394	3
β-strand	396-398	3	11
β-strand	407-409	3	11
α-helix	410-412	3
β-strand	418	1	10
β-strand	421-424	4	1
β-strand	430-434	5	1
β-strand	439-444	6	1

Chain C: 15 helices, 18 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	22-24	3
α-helix	25-40	16
β-strand	45-48	4	12
α-helix	49	1
β-strand	52-55	4	13
β-strand	57	1	14
α-helix	62-72	11
β-strand	80-82	3	13
α-helix	93-106	14
β-strand	111-113	3	13
α-helix	121-126	6
α-helix	129-137	9
α-helix	141-150	10
β-strand	156-159	4	12
β-strand	163-166	4	12
α-helix	177-182	6
α-helix	188-190	3
α-helix	193-198	6
β-strand	202-203	2	15
β-strand	211	1	16
β-strand	218	1	16
β-strand	219-220	2	15
α-helix	222-232	11
β-strand	236-239	4	12
β-strand	248-251	4	12
β-strand	256-259	4	12
β-strand	260	1	14
α-helix	265-267	3
β-strand	273-278	6	13
β-strand	284-289	6	13
β-strand	299-301	3	6
α-helix	304-305	2

Chain D: 2 helices, 0 β-strands

Element	Residues	Length	Sheet
α-helix	616-619	4
α-helix	620-630	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)
Retinoblastoma-like protein 1	D	protein	78	Homo sapiens	P28749 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9C6B_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

>9C6B_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

>9C6B_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (chains C)
GHMDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDV
HGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNH
ESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLD
HIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVS
RAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEP
HVTRRTPDYFL

Sequence of entity 4 (D), FASTA

>9C6B_4 Retinoblastoma-like protein 1 (chains D)
GHMPMSPLMHPRVKEVRTDSGSLRRDMQPLSPISVHERYSSPTAGSAKRRLFGEDPPKEM
LMDKIITEGTKLKIAPSS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	1
FE2	FE (II) ion	Fe	1

Primary citation

Cryo-EM structures of PP2A:B55 with p107 and Eya3 define substrate recruitment. Padi, S.K.R., Godek, R.J., Peti, W. et al. Nat Struct Mol Biol (2025) 32:1373-1382. DOI 10.1038/s41594-025-01535-3 · 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
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
4I5N 2.8 Å, Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6…

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