4I5L: PDB entry 4I5L

Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation. Determined by X-ray diffraction at 2.43 Å resolution. Released 8 May 2013.

Method: X-ray diffraction
Resolution: 2.43 Å
Organisms: Homo sapiens, Microcystis aeruginosa
Chains: 8
Atoms: 20,426
Mol. weight: 299.71 kDa
Ligands: MLI, MN, CA
Released: 8 May 2013

Explore 4I5L in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4I5L contains 213 α-helices and 48 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: 62 helices, 0 β-strands

Element	Residues	Length
α-helix	11-19	9
α-helix	25-33	9
α-helix	35-42	8
α-helix	44-46	3
α-helix	47-51	5
α-helix	52-57	6
α-helix	63-73	11
α-helix	77-80	4
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	141-148	8
α-helix	151-154	4
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	223-234	12
α-helix	237-239	3
α-helix	240-243	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	306-311	6
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-334	8
α-helix	339-346	8
α-helix	349-352	4
α-helix	353-360	8
α-helix	361-365	5
α-helix	366-373	8
α-helix	378-385	8
α-helix	389-394	6
α-helix	397-399	3
α-helix	401-412	12
α-helix	417-434	18
α-helix	436-438	3
α-helix	439-443	5
α-helix	444-450	7
α-helix	456-473	18
α-helix	475-481	7
α-helix	483-488	6
α-helix	489-491	3
α-helix	495-508	14
α-helix	513-520	8
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: 29 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	141-152	12
α-helix	156-158	3
β-strand	159-160	2	1
α-helix	162-164	3
α-helix	165-171	7
α-helix	176-178	3
α-helix	179-185	7
α-helix	188-190	3
β-strand	194-195	2	1
α-helix	196-209	14
α-helix	213-221	9
α-helix	223	1
β-strand	228-229	2	2
α-helix	231-234	4
α-helix	235-244	10
α-helix	246-251	6
α-helix	256-273	18
β-strand	281-282	2	2
α-helix	283-288	6
α-helix	291-297	7
α-helix	304-306	3
α-helix	313-324	12
β-strand	333-335	3	3
α-helix	336-345	10
β-strand	347	1	4
α-helix	349-355	7
α-helix	365-369	5
β-strand	371-373	3	3
α-helix	374-385	12
α-helix	390-400	11
β-strand	407-408	2	5
α-helix	410-425	16
α-helix	429-433	5
α-helix	434-445	12
β-strand	453-454	2	5
α-helix	455-461	7
α-helix	464-472	9
β-strand	473	1	4
α-helix	474-477	4

Chain C: 15 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	22-24	3
α-helix	25-39	15
β-strand	45-48	4	6
α-helix	49	1
β-strand	52-55	4	7
α-helix	62-72	11
β-strand	80-82	3	7
α-helix	93-106	14
β-strand	111-113	3	7
α-helix	121-127	7
α-helix	129-137	9
α-helix	141-150	10
β-strand	156-159	4	6
β-strand	163-166	4	6
α-helix	177-182	6
α-helix	188-190	3
α-helix	194-200	7
β-strand	202-203	2	8
β-strand	209-211	3	8
β-strand	218-220	3	8
α-helix	222-232	11
β-strand	236-239	4	6
β-strand	248-251	4	6
β-strand	256-259	4	6
α-helix	265-267	3
β-strand	273-278	6	7
β-strand	284-289	6	7
α-helix	290-293	4

Chain D: 61 helices, 0 β-strands

Element	Residues	Length
α-helix	10-18	9
α-helix	19-21	3
α-helix	25-33	9
α-helix	35-41	7
α-helix	44-46	3
α-helix	47-51	5
α-helix	52-57	6
α-helix	63-73	11
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	141-148	8
α-helix	151-154	4
α-helix	160-174	15
α-helix	179-193	15
α-helix	198-200	3
α-helix	201-205	5
α-helix	206-212	7
α-helix	218-221	4
α-helix	224-234	11
α-helix	240-243	4
α-helix	245-252	8
α-helix	257-265	9
α-helix	267-278	12
α-helix	279-283	5
α-helix	284-291	8
α-helix	296-303	8
α-helix	306-311	6
α-helix	318-321	4
α-helix	322-326	5
α-helix	327-334	8
α-helix	339-346	8
α-helix	349-352	4
α-helix	353-360	8
α-helix	361-365	5
α-helix	366-373	8
α-helix	378-385	8
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	444-450	7
α-helix	456-473	18
α-helix	475-481	7
α-helix	483-488	6
α-helix	489-491	3
α-helix	495-516	22
α-helix	517-521	5
α-helix	522-527	6
α-helix	528-530	3
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 E: 30 helices, 10 β-strands

Element	Residues	Length	Sheet
α-helix	121-124	4
α-helix	141-152	12
α-helix	156-158	3
β-strand	159-160	2	9
α-helix	162-164	3
α-helix	165-171	7
α-helix	176-178	3
α-helix	179-185	7
α-helix	188-191	4
β-strand	194-195	2	9
α-helix	196-209	14
α-helix	213-221	9
α-helix	223	1
β-strand	228-229	2	10
α-helix	231-234	4
α-helix	235-244	10
α-helix	246-251	6
α-helix	256-273	18
β-strand	281-282	2	10
α-helix	283-287	5
α-helix	291-300	10
α-helix	304-306	3
α-helix	313-324	12
β-strand	333-335	3	11
α-helix	336-340	5
β-strand	347	1	12
α-helix	349-354	6
α-helix	365-369	5
β-strand	371-373	3	11
α-helix	374-385	12
α-helix	390-400	11
β-strand	408	1	13
α-helix	410-426	17
α-helix	429-433	5
α-helix	434-445	12
β-strand	453	1	13
α-helix	455-461	7
α-helix	464-472	9
β-strand	473	1	12
α-helix	474-477	4

Chain F: 16 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	3-18	16
α-helix	22-24	3
α-helix	25-39	15
β-strand	45-48	4	14
α-helix	49	1
β-strand	52-55	4	15
α-helix	62-72	11
β-strand	80-82	3	15
α-helix	93-106	14
β-strand	111-113	3	15
α-helix	121-126	6
α-helix	129-137	9
α-helix	141-150	10
β-strand	156-159	4	14
β-strand	163-166	4	14
α-helix	177-182	6
α-helix	188-190	3
α-helix	194-200	7
β-strand	202-203	2	16
β-strand	209-211	3	16
β-strand	218-220	3	16
α-helix	222-232	11
β-strand	236-239	4	14
β-strand	248-251	4	14
α-helix	252-254	3
β-strand	256-259	4	14
α-helix	265-267	3
β-strand	273-278	6	15
β-strand	284-289	6	15
α-helix	290-293	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform	A, D	protein	584	Homo sapiens	P30153 (AlphaFold model)
Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division…	B, E	protein	413	Homo sapiens	Q99741 (AlphaFold model), Q9Y5P8 (AlphaFold model)
Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha	C, F	protein	311	Homo sapiens	P67775 (AlphaFold model)
Microcystin-LR (MCLR) bound form	G, H	protein	7	Microcystis aeruginosa

Sequence of entity 1 (A, D), FASTA

>4I5L_1 Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform (chains A, D)
GSMSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEV
LLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLE
AHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAA
ASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVM
PTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHK
VKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHL
LPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIE
YMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPK
VLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQ
KIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

Sequence of entity 2 (B, E), FASTA

>4I5L_2 Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct (chains B, E)
GSSQSIPTFYFPRGRPQDSVNVDAVISKIESTFARFPHERATMDDMGLVAKACGCPLYWK
GPLFYGAGGERTGSVSVHKFVAMWRKILQNCHDDAAKFVHLLMSPGCNYLVQEDFVPFLQ
DVVNTHPGLSFLKEASEFHSRYITTVIQRIFYAVNRSWSGRITCAELRRSSFLQNVALLE
EEADINQLTEFFSYEHFYVIYCKFWELDTDHDLLIDADDLARHNDHALSTKMIDRIFSGA
VTRGRKVQKEGKISYADFVWFLISEEDKKTPTSIEYWFRCMDLDGDGALSMFELEYFYEE
QCRRLDSMAIEALPFQDCLCQMLDLVKPRTEGKITLQDLKRCKLANVFFDTFFNIEKYLD
HEQKEQISLLRSTGNASDSSSDSSSSEGDGTVLPPCSPPKQGKKENGPPHSHT

Sequence of entity 3 (C, F), FASTA

>4I5L_3 Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha (chains C, F)
GSMDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDV
HGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNH
ESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLD
HIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVS
RAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEP
HVTRRTPDYFL

Sequence of entity 4 (G, H), FASTA

>4I5L_4 Microcystin-LR (MCLR) bound form (chains G, H)
ALDRXEA

Ligands and cofactors

ID	Name	Formula	Copies
MLI	Malonate ion	C3 H2 O4	3
MN	Manganese (II) ion	Mn	4
CA	Calcium ion	Ca	4

Water and common crystallization additives (PEG) are not listed.

Primary citation

Structure of the Ca(2+)-dependent PP2A heterotrimer and insights into Cdc6 dephosphorylation. Wlodarchak, N., Guo, F., Satyshur, K.A. et al. Cell Res (2013) 23:931-946. DOI 10.1038/cr.2013.77 · 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
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
4I5N 2.8 Å, Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6…

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