3DW8: PDB entry 3DW8

Structure of a Protein Phosphatase 2A Holoenzyme with B55 subunit. Determined by X-ray diffraction at 2.85 Å resolution. Released 7 Oct 2008.

Method: X-ray diffraction
Resolution: 2.85 Å
Organisms: Homo sapiens, Cyanobacteria
Chains: 8
Atoms: 20,717
Mol. weight: 306.54 kDa
Ligands: MN
Released: 7 Oct 2008

Explore 3DW8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DW8 contains 170 α-helices and 99 β-strands across 6 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	11-19	9
α-helix	25-32	8
α-helix	35-41	7
α-helix	46	1
α-helix	47-51	5
α-helix	52-57	6
α-helix	63-74	12
α-helix	78-80	3
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	160-173	14
α-helix	179-193	15
α-helix	200-203	4
α-helix	205-212	8
α-helix	218-232	15
α-helix	240-243	4
α-helix	245-251	7
α-helix	257-265	9
α-helix	267-274	8
α-helix	276-278	3
α-helix	279-283	5
α-helix	284-290	7
α-helix	296-303	8
α-helix	306-310	5
α-helix	315-321	7
α-helix	322-326	5
α-helix	327-330	4
α-helix	339-345	7
α-helix	353-363	11
α-helix	366-373	8
α-helix	378-386	9
α-helix	389-392	4
α-helix	398-401	4
α-helix	404-412	9
α-helix	417-424	8
α-helix	427-432	6
α-helix	436-438	3
α-helix	439-443	5
α-helix	444-447	4
α-helix	450-452	3
α-helix	456-467	12
α-helix	474-480	7
α-helix	483-486	4
α-helix	488-491	4
α-helix	495-508	14
α-helix	513-516	4
α-helix	517-521	5
α-helix	522-528	7
α-helix	534-547	14
α-helix	555-558	4
α-helix	560-567	8
α-helix	573-580	8

Chain B: 12 helices, 33 β-strands

Element	Residues	Length	Sheet
β-strand	13-16	4	1
α-helix	27-29	3
β-strand	31-36	6	2
β-strand	42-47	6	2
β-strand	51-57	7	2
α-helix	69-70	2
β-strand	71-78	8	2
β-strand	83-85	3	3
α-helix	86-88	3
β-strand	90-92	3	3
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	156-172	17	4
β-strand	182-185	4	5
β-strand	191-195	5	5
β-strand	199-204	6	5
β-strand	207-216	10	5
α-helix	222-224	3
β-strand	229-234	6	6
β-strand	241-246	6	6
β-strand	251-255	5	6
β-strand	267-269	3	6
α-helix	280-284	5
β-strand	288-293	6	7
β-strand	299-304	6	7
β-strand	307-312	6	7
β-strand	323-324	2	7
α-helix	327-329	3
α-helix	333-338	6
α-helix	341-343	3
β-strand	348-350	3	8
β-strand	356-360	5	8
β-strand	365-370	6	8
β-strand	376-380	5	8
α-helix	390	1
β-strand	391	1	1
α-helix	392	1
β-strand	397-398	2	9
β-strand	408-409	2	9
α-helix	410-412	3
β-strand	421-424	4	1
β-strand	430-434	5	1
β-strand	439-443	5	1

Chain C: 15 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	7-18	12
α-helix	25-40	16
β-strand	45-48	4	10
α-helix	49	1
α-helix	51	1
β-strand	52-55	4	11
β-strand	57	1	12
α-helix	62-72	11
β-strand	80-82	3	11
α-helix	93-106	14
β-strand	111-113	3	11
α-helix	121-126	6
α-helix	129-137	9
α-helix	141-151	11
β-strand	156-159	4	10
β-strand	163-166	4	10
α-helix	177-182	6
α-helix	188-190	3
α-helix	194-200	7
β-strand	202-203	2	13
β-strand	209-211	3	13
β-strand	218-220	3	13
α-helix	222-231	10
β-strand	236-239	4	10
β-strand	248-251	4	10
β-strand	256-259	4	10
β-strand	260	1	12
α-helix	265-267	3
β-strand	273-278	6	11
β-strand	284-289	6	11
α-helix	290-292	3

Chain D: 58 helices, 0 β-strands

Element	Residues	Length
α-helix	10-19	10
α-helix	25-32	8
α-helix	35-41	7
α-helix	46	1
α-helix	47-51	5
α-helix	52-57	6
α-helix	63-73	11
α-helix	78-80	3
α-helix	86-89	4
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	160-174	15
α-helix	179-186	8
α-helix	189-193	5
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-212	7
α-helix	218-232	15
α-helix	237-243	7
α-helix	245-251	7
α-helix	257-265	9
α-helix	267-278	12
α-helix	279-283	5
α-helix	284-290	7
α-helix	296-303	8
α-helix	306-310	5
α-helix	315-321	7
α-helix	322-326	5
α-helix	327-330	4
α-helix	339-349	11
α-helix	353-363	11
α-helix	366-373	8
α-helix	380-383	4
α-helix	389-392	4
α-helix	398-401	4
α-helix	405-412	8
α-helix	417-432	16
α-helix	437-438	2
α-helix	439-443	5
α-helix	444-449	6
α-helix	450-452	3
α-helix	456-467	12
α-helix	474-480	7
α-helix	483-488	6
α-helix	495-508	14
α-helix	509-511	3
α-helix	513-516	4
α-helix	517-521	5
α-helix	522-528	7
α-helix	534-547	14
α-helix	555-558	4
α-helix	560-567	8
α-helix	573-580	8

Chain E: 12 helices, 34 β-strands

Element	Residues	Length	Sheet
β-strand	13-18	6	14
α-helix	27-29	3
β-strand	31-36	6	15
β-strand	42-47	6	15
β-strand	51-57	7	15
α-helix	69-70	2
β-strand	71-78	8	15
β-strand	83-85	3	16
β-strand	90-92	3	16
β-strand	98-101	4	17
α-helix	102-103	2
β-strand	109-114	6	17
β-strand	119-132	14	17
β-strand	156-172	17	17
β-strand	182-185	4	18
β-strand	191-195	5	18
β-strand	199-204	6	18
β-strand	207-216	10	18
α-helix	222-224	3
β-strand	229-234	6	19
β-strand	241-246	6	19
β-strand	251-255	5	19
α-helix	266	1
β-strand	267-269	3	19
α-helix	280-284	5
β-strand	288-293	6	20
β-strand	299-304	6	20
β-strand	307-312	6	20
β-strand	315	1	20
β-strand	323-324	2	20
α-helix	327-332	6
α-helix	333-338	6
α-helix	341-343	3
β-strand	348-350	3	21
β-strand	356-360	5	21
β-strand	365-370	6	21
β-strand	376-380	5	21
α-helix	390	1
β-strand	391	1	14
α-helix	392	1
β-strand	397	1	22
β-strand	408	1	22
α-helix	410-412	3
β-strand	422-424	3	14
β-strand	430-434	5	14
β-strand	439-443	5	14

Chain F: 16 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	8-18	11
α-helix	25-40	16
β-strand	45-48	4	23
α-helix	49	1
β-strand	52-55	4	24
β-strand	57	1	25
α-helix	62-72	11
β-strand	80-82	3	24
α-helix	93-106	14
β-strand	111-113	3	24
α-helix	114-116	3
α-helix	121-126	6
α-helix	129-134	6
α-helix	141-152	12
β-strand	156-159	4	23
β-strand	163-166	4	23
α-helix	177-182	6
α-helix	188-190	3
α-helix	194-198	5
β-strand	202-203	2	26
β-strand	210-211	2	26
β-strand	218-220	3	26
α-helix	222-231	10
β-strand	236-239	4	23
β-strand	248-251	4	23
α-helix	252-254	3
β-strand	256-259	4	23
β-strand	260	1	25
α-helix	265-267	3
β-strand	273-278	6	24
β-strand	284-289	6	24
α-helix	290-292	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	A, D	protein	582	Homo sapiens	P30153 (AlphaFold model)
Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform	B, E	protein	447	Homo sapiens	P63151 (AlphaFold model)
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform	C, F	protein	309	Homo sapiens	P67775 (AlphaFold model)
microcystin LR	G, H	protein	7	Cyanobacteria

Sequence of entity 1 (A, D), FASTA

>3DW8_1 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (chains A, D)
MSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLL
ALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAH
FVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAAS
KLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPT
LRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVK
EFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHLLP
LFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIEYM
PLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVL
AMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKI
GPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

Sequence of entity 2 (B, E), FASTA

>3DW8_2 Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform (chains B, E)
MAGAGGGNDIQWCFSQVKGAVDDDVAEADIISTVEFNHSGELLATGDKGGRVVIFQQEQE
NKIQSHSRGEYNVYSTFQSHEPEFDYLKSLEIEEKINKIRWLPQKNAAQFLLSTNDKTIK
LWKISERDKRPEGYNLKEEDGRYRDPTTVTTLRVPVFRPMDLMVEASPRRIFANAHTYHI
NSISINSDYETYLSADDLRINLWHLEITDRSFNIVDIKPANMEELTEVITAAEFHPNSCN
TFVYSSSKGTIRLCDMRASALCDRHSKLFEEPEDPSNRSFFSEIISSISDVKFSHSGRYM
MTRDYLSVKVWDLNMENRPVETYQVHEYLRSKLCSLYENDCIFDKFECCWNGSDSVVMTG
SYNNFFRMFDRNTKRDITLEASRENNKPRTVLKPRKVCASGKRKKDEISVDSLDFNKKIL
HTAWHPKENIIAVATTNNLYIFQDKVN

Sequence of entity 3 (C, F), FASTA

>3DW8_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (chains C, F)
MDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHG
QFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHES
RQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHI
RALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRA
HQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHV
TRRTPDYFL

Sequence of entity 4 (G, H), FASTA

>3DW8_4 microcystin LR (chains G, H)
ALDRXEX

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	4

Primary citation

Structure of a protein phosphatase 2A holoenzyme: insights into B55-mediated Tau dephosphorylation. Xu, Y., Chen, Y., Zhang, P. et al. Mol Cell (2008) 31:873-885. DOI 10.1016/j.molcel.2008.08.006 · 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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