7SOY: PP2A-B56gamma1 holoenzyme-PME-1 complex

The structure of the PP2A-B56gamma1 holoenzyme-PME-1 complex. Determined by electron microscopy at 3.4 Å resolution. Released 31 Aug 2022.

Method: Electron microscopy
Resolution: 3.4 Å
Organism: Homo sapiens
Chains: 4
Atoms: 12,180
Mol. weight: 196.06 kDa
Released: 31 Aug 2022

Explore 7SOY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7SOY contains 109 α-helices and 31 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: 56 helices, 0 β-strands

Element	Residues	Length
α-helix	11-21	11
α-helix	25-33	9
α-helix	35-41	7
α-helix	44-46	3
α-helix	47-51	5
α-helix	52-58	7
α-helix	63-75	13
α-helix	82-84	3
α-helix	86-98	13
α-helix	102-118	17
α-helix	121-123	3
α-helix	124-128	5
α-helix	129-136	8
α-helix	141-154	14
α-helix	160-174	15
α-helix	179-195	17
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-213	8
α-helix	218-234	17
α-helix	237-240	4
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	306-312	7
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-334	8
α-helix	339-349	11
α-helix	352-356	5
α-helix	358-360	3
α-helix	361-365	5
α-helix	366-373	8
α-helix	378-386	9
α-helix	389-394	6
α-helix	397-412	16
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	475-480	6
α-helix	482-489	8
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	553-555	3
α-helix	556-560	5
α-helix	561-568	8
α-helix	573-586	14

Chain B: 23 helices, 0 β-strands

Element	Residues	Length
α-helix	35-50	16
α-helix	63-82	20
α-helix	91-103	13
α-helix	106-109	4
α-helix	131-146	16
α-helix	152-155	4
α-helix	161-169	9
α-helix	170-172	3
α-helix	176-192	17
α-helix	197-210	14
α-helix	211-215	5
α-helix	221-233	13
α-helix	241-246	6
α-helix	247-251	5
α-helix	252-256	5
α-helix	260-277	18
α-helix	282-291	10
α-helix	298-314	17
α-helix	317-335	19
α-helix	340-351	12
α-helix	353-361	9
α-helix	363-379	17
α-helix	384-400	17

Chain C: 13 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	7-18	12
α-helix	25-39	15
β-strand	45-48	4	1
α-helix	49	1
β-strand	52-57	6	2
α-helix	62-72	11
β-strand	80-84	5	2
α-helix	93-106	14
β-strand	111-113	3	2
α-helix	121-126	6
α-helix	129-137	9
α-helix	141-152	12
β-strand	156-159	4	1
β-strand	163-165	3	1
α-helix	177-182	6
α-helix	193-200	8
β-strand	203	1	3
β-strand	210-211	2	4
β-strand	218-219	2	4
β-strand	220	1	3
α-helix	222-232	11
β-strand	236-239	4	1
β-strand	248-251	4	1
β-strand	256-259	4	1
α-helix	265-267	3
β-strand	273-278	6	2
β-strand	284-289	6	2
α-helix	290-292	3

Chain P: 17 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	42-45	4
α-helix	46-49	4
β-strand	52-54	3	5
β-strand	57-59	3	6
β-strand	64-66	3	6
β-strand	69-72	4	5
β-strand	78-82	5	5
α-helix	89-92	4
α-helix	93-102	10
β-strand	103	1	7
β-strand	107-109	3	5
α-helix	111-112	2
β-strand	119	1	6
α-helix	128-142	15
α-helix	147-149	3
β-strand	150-155	6	5
α-helix	157-168	12
β-strand	177-180	4	5
α-helix	184-189	6
α-helix	191-199	9
β-strand	205	1	8
α-helix	208-218	11
α-helix	224-234	11
β-strand	235-237	3	8
β-strand	285-287	3	8
α-helix	291-301	11
α-helix	305-311	7
β-strand	316-320	5	5
α-helix	328-335	8
β-strand	340-343	4	5
α-helix	351-354	4
α-helix	356-370	15
β-strand	375	1	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	A	protein	589	Homo sapiens	P30153 (AlphaFold model)
Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform	B	protein	449	Homo sapiens	Q13362 (AlphaFold model)
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	C	protein	309	Homo sapiens	P67775 (AlphaFold model)
Protein phosphatase methylesterase 1	P	protein	386	Homo sapiens	Q9Y570 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7SOY_1 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (chains A)
MAAADGDDSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIY
DEDEVLLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHS
PSDLEAHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPM
VRRAAASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDL
EALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRA
AASHKVKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDN
TIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVR
LAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHA
TIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNV
AKSLQKIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

Sequence of entity 2 (B), FASTA

>7SOY_2 Isoform Gamma-1 of Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform (chains B)
MLTCNKAGSRMVVDAANSNGPFQPVVLLHIRDVPPADQEKLFIQKLRQCCVLFDFVSDPL
SDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMFAVNMFRTLPPSSNPTGAEFDP
EEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLQLLELFDSEDPRERD
FLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLK
EEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPK
EVMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLIS
DNAAKILPIMFPSLYRNSKTHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEK
LKMKEREEAWVKIENLAKANPQVLKKRIT

Sequence of entity 3 (C), FASTA

>7SOY_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (chains C)
MDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHG
QFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHES
RQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHI
RALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRA
HQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHV
TRRTPDYFL

Sequence of entity 4 (P), FASTA

>7SOY_4 Protein phosphatase methylesterase 1 (chains P)
MSALEKSMHLGRLPSRPPLPGSGGSQSGAKMRMGPGRKRDFSPVPWSQYFESMEDVEVEN
ETGKDTFRVYKSGSEGPVLLLLHGGGHSALSWAVFTAAIISRVQCRIVALDLRSHGETKV
KNPEDLSAETMAKDVGNVVEAMYGDLPPPIMLIGHAMGGAIAVHTASSNLVPSLLGLCMI
DVVEGTAMDALNSMQNFLRGRPKTFKSLENAIEWSVKSGQIRNLESARVSMVGQVKQCEG
ITSPEGSKSIVEGIIEEEEEDEEGSESISKRKKEDDMETKKDHPYTWRIELAKTEKYWDG
WFRGLSNLFLSCPIPKLLLLAGVDRLDKDLTIGQMQGKFQMQVLPQCGHAVHEDAPDKVA
EAVATFLIRHRFAEPIGGFQCVFPGC

Primary citation

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition. Li, Y., Balakrishnan, V.K., Rowse, M. et al. Elife (2022) 11. DOI 10.7554/eLife.79736 · 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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