2nyl

Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated

Method: X-RAY DIFFRACTION

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

Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 1 （Q13362） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform × 1 （P67775） microcystin LR × 1 MANGANESE (II) ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 1 （Q13362） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform × 1 （P67775） microcystin LR × 1 MANGANESE (II) ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q96DH3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–582； UniProt 8–589 Author chain D； PDBConstruct 1–582； UniProt 8–589

Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

Homo sapiens

UniProt Q13362

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform × 1 （Q96DH3） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform × 1 （P67775） microcystin LR × 1 MANGANESE (II) ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform × 1 （Q96DH3） Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform × 1 （P67775） microcystin LR × 1 MANGANESE (II) ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	2A5G_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–388； UniProt 38–425 Author chain E； PDBConstruct 1–388； UniProt 38–425

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

Homo sapiens

UniProt P67775

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform × 1 （Q96DH3） Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 1 （Q13362） microcystin LR × 1 MANGANESE (II) ION × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform × 1 （Q96DH3） Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform × 1 （Q13362） microcystin LR × 1 MANGANESE (II) ION × 2	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 1–293； UniProt 2–294 Author chain F； PDBConstruct 1–293； UniProt 2–294

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	2nyl
Deposition date deposition_date	2006-11-20
Structure title title	Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated
Keywords keywords	HEAT repeat, HYDROLASE-HYDROLASE INHIBITOR COMPLEX; HYDROLASE/HYDROLASE INHIBITOR
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.

2nyl__assembly_1__model_1

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

Download this curve (.dat)

2nyl__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2nyl__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	37.10 Å
Rg (electron density)	36.36 Å
Total Rg	36.98 Å
Atom count	10106
Residues	1241
Excluded volume	181500 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2nyl__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2nyl__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 (5)

Entity 1 Entity 1 polymer

Description description	Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform
Molecular weight formula_weight	65356.3 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	20212

DSLYPIAVLIDELRNEDVQLRLNSIKKLSTIALALGVERTRSELLPFLTDTIYDEDEVLLALAEQLGTFTTLVGGPEYVHCLLPPLESLATVEETVVRDKAVESLRAISHEHSPSDLEAHFVPLVKRLAGGDWFTSRTSACGLFSVCYPRVSSAVKAELRQYFRNLCSDDTPMVRRAAASKLGEFAKVLELDNVKSEIIPMFSNLASDEQDSVRLLAVEACVNIAQLLPQEDLEALVMPTLRQAAEDKSWRVRYMVADKFTELQKAVGPEITKTDLVPAFQNLMKDCEAEVRAAASHKVKEFCENLSADCRENVIMSQILPCIKELVSDANQHVKSALASVIMGLSPILGKDNTIEHLLPLFLAQLKDECPEVRLNIISNLDCVNEVIGIRQLSQSLLPAIVELAEDAKWRVRLAIIEYMPLLAGQLGVEFFDEKLNSLCMAWLVDHVYAIREAATSNLKKLVEKFGKEWAHATIIPKVLAMSGDPNYLHRMTTLFCINVLSEVCGQDITTKHMLPTVLRMAGDPVANVRFNVAKSLQKIGPILDNSTLQSEVKPILEKLTQDQDVDVKYFAQEALTVLSLA

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 BL21(DE3)

Entity 2 Entity 2 polymer

Description description	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform
Molecular weight formula_weight	46467.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

QEKLFIQKLRQCCVLFDFVSDPLSDLKWKEVKRAALSEMVEYITHNRNVITEPIYPEVVHMFAVNMFRTLPPSSNPTGAEFDPEEDEPTLEAAWPHLQLVYEFFLRFLESPDFQPNIAKKYIDQKFVLQLLELFDSEDPRERDFLKTTLHRIYGKFLGLRAYIRKQINNIFYRFIYETEHHNGIAELLEILGSIINGFALPLKEEHKIFLLKVLLPLHKVKSLSVYHPQLAYCVVQFLEKDSTLTEPVVMALLKYWPKTHSPKEVMFLNELEEILDVIEPSEFVKIMEPLFRQLAKCVSSPHFQVAERALYYWNNEYIMSLISDNAAKILPIMFPSLYRNSKTHWNKTIHGLIYNALKLFMEMNQKLFDDCTQQFKAEKLKEKLKMKE

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 BL21(DE3)

Entity 3 Entity 3 polymer

Description description	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform
Molecular weight formula_weight	33674.9 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

DEKVFTKELDQWIEQLNECKQLSESQVKSLCEKAKEILTKESNVQEVRCPVTVCGDVHGQFHDLMELFRIGGKSPDTNYLFMGDYVDRGYYSVETVTLLVALKVRYRERITILRGNHESRQITQVYGFYDECLRKYGNANVWKYFTDLFDYLPLTALVDGQIFCLHGGLSPSIDTLDHIRALDRLQEVPHEGPMCDLLWSDPDDRGGWGISPRGAGYTFGQDISETFNHANGLTLVSRAHQLVMEGYNWCHDRNVVTIFSAPNYCYRCGNQAAIMELDDTLKYSFLQFDPAPR

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 4 Entity 4 polymer

Description description	microcystin LR
Molecular weight formula_weight	1014.2 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

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

ALDRXEX

Entity 5 Entity 5 non-polymer

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

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d2nyla1
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	d2nylb1
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.118.1.20 — B56-like

Domain ID domain_id	d2nylc1
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	d2nyld1
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	d2nyle1
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.118.1.20 — B56-like

Domain ID domain_id	d2nylf1
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 (6 domains)

Domain ID domain_id	2nylA00
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	2nylB00
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	2nylC00
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	2nylD00
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	2nylE00
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	2nylF00
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	108.480 Å
Unit-cell length b length_b	159.850 Å
Unit-cell length c length_c	270.370 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	3.800 Å
Low-resolution limit resolution_low	100.000 Å
R factor r_factor	0.3000
R_work r_work	0.2820
R_free r_free	0.3350

Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated

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

Protein phosphatase 2, regulatory subunit A (PR 65), alpha isoform

State in the Current Structure

Other States of the Same Protein in the Database

Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit gamma isoform

State in the Current Structure

Other States of the Same Protein in the Database

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

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2nyl__assembly_1__model_1

2nyl__assembly_1__model_1 | I(q)

2nyl__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 (5)

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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Crystal structure of Protein Phosphatase 2A (PP2A) holoenzyme with the catalytic subunit carboxyl terminus truncated

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

Protein phosphatase 2, regulatory subunit A (PR 65), 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 56 kDa regulatory subunit gamma 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 catalytic subunit 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

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

2nyl__assembly_1__model_1

2nyl__assembly_1__model_1 | I(q)

2nyl__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 (5)

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

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

CATH v4.4 (6 domains)

7. Citations (1)