4i5l

Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation

Method: X-RAY DIFFRACTION

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ; × 1 （Q99741,Q9Y5P8） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 8 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ; × 1 （Q99741,Q9Y5P8） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 3 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	2AAA_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–584； UniProt 9–589 Author chain D； PDBConstruct 4–584； UniProt 9–589

;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ;

Homo sapiens

UniProt Q99741

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 8 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 3 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDC6_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 393–413； UniProt 70–90 Author chain E； PDBConstruct 393–413； UniProt 70–90

;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ;

Homo sapiens

UniProt Q9Y5P8

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 8 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha × 1 （P67775） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 3 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	P2R3B_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–371； UniProt 122–490 Author chain E； PDBConstruct 3–371； UniProt 122–490

Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha

Homo sapiens

UniProt P67775

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） ;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ; × 1 （Q99741,Q9Y5P8） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 8 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 1 water × 3	Consistent with protein count
2	Insufficient information	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform × 1 （P30153） ;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ; × 1 （Q99741,Q9Y5P8） Microcystin-LR (MCLR) bound form × 1 DI(HYDROXYETHYL)ETHER × 3 CALCIUM ION × 2 MANGANESE (II) ION × 2 MALONATE ION × 2 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	PP2AA_HUMAN
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain C； PDBConstruct 3–311； UniProt 1–309 Author chain F； PDBConstruct 3–311； UniProt 1–309

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4i5l
Deposition date deposition_date	2012-11-28
Structure title title	Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation
Keywords keywords	EF Hand, Phosphatase, CDC6 (Substrate), HYDROLASE-TOXIN complex; HYDROLASE/TOXIN
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

4i5l__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4i5l__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4i5l__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	37.80 Å
Rg (electron density)	37.35 Å
Total Rg	37.79 Å
Atom count	9958
Residues	1235
Excluded volume	178180 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4i5l__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4i5l__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform
Molecular weight formula_weight	64906.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	20426

GSMSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ;
Molecular weight formula_weight	47227.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

GSSQSIPTFYFPRGRPQDSVNVDAVISKIESTFARFPHERATMDDMGLVAKACGCPLYWKGPLFYGAGGERTGSVSVHKFVAMWRKILQNCHDDAAKFVHLLMSPGCNYLVQEDFVPFLQDVVNTHPGLSFLKEASEFHSRYITTVIQRIFYAVNRSWSGRITCAELRRSSFLQNVALLEEEADINQLTEFFSYEHFYVIYCKFWELDTDHDLLIDADDLARHNDHALSTKMIDRIFSGAVTRGRKVQKEGKISYADFVWFLISEEDKKTPTSIEYWFRCMDLDGDGALSMFELEYFYEEQCRRLDSMAIEALPFQDCLCQMLDLVKPRTEGKITLQDLKRCKLANVFFDTFFNIEKYLDHEQKEQISLLRSTGNASDSSSDSSSSEGDGTVLPPCSPPKQGKKENGPPHSHT

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha
Molecular weight formula_weight	35780.3 kDa
EC 编号 ec_number	3.1.3.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

GSMDEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPRRGEPHVTRRTPDYFL

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Trichoplusia ni

Entity 4 Entity 4 polymer

Description description	Microcystin-LR (MCLR) bound form
Molecular weight formula_weight	1016.2 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	G,H

ALDRXEA

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 6 Entity 6 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 non-polymer

Description description	MALONATE ION
Molecular weight formula_weight	102.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	531

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d4i5la1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

Domain ID domain_id	d4i5la2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4i5lc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.3 — Protein serine/threonine phosphatase

Domain ID domain_id	d4i5ld1
Class class	a — All alpha proteins
Fold Fold fold	a.118 — alpha-alpha superhelix
Superfamily Superfamily superfamily	a.118.1 — ARM repeat
Family Family family	a.118.1.2 — HEAT repeat

Domain ID domain_id	d4i5ld2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4i5lf_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamily	d.159.1 — Metallo-dependent phosphatases
Family Family family	d.159.1.3 — Protein serine/threonine phosphatase

CATH v4.4 (10 domains)

Domain ID domain_id	4i5lA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	4i5lB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	4i5lB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	4i5lB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4i5lC00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

Domain ID domain_id	4i5lD00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	10 — Leucine-rich Repeat Variant
Homologous superfamily homologous superfamily	10 — Leucine-rich Repeat Variant

Domain ID domain_id	4i5lE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	230 —

Domain ID domain_id	4i5lE02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	220 —

Domain ID domain_id	4i5lE03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	238 — Recoverin; domain 1
Homologous superfamily homologous superfamily	10 — EF-hand

Domain ID domain_id	4i5lF00
Class class	3 — Alpha Beta
Architecture architecture	60 — 4-Layer Sandwich
Topology topology	21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily	10 — Metallo-dependent phosphatases

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Unit-cell length a length_a	94.234 Å
Unit-cell length b length_b	101.071 Å
Unit-cell length c length_c	343.396 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.430 Å
Low-resolution limit resolution_low	49.850 Å
R factor r_factor	0.1815
R_work r_work	0.1791
R_free r_free	0.2278

Structural mechanism of trimeric PP2A holoenzyme involving PR70: insight for Cdc6 dephosphorylation

1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

;Serine/threonine-protein phosphatase 2A regulatory subunit B'' subunit beta - Cell division control protein 6 homolog chimeric construct ;

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform, PP2A-alpha

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

4i5l__assembly_1__model_1

4i5l__assembly_1__model_1 | I(q)

4i5l__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (6 domains)

CATH v4.4 (10 domains)

7. Citations (1)