3v4y

Crystal Structure of the first Nuclear PP1 holoenzyme

Method: X-RAY DIFFRACTION Dmax: 110.7 Å Quality: EXCELLENT

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

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit

Homo sapiens

UniProt P62136

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 7–307 Fragment:PP1 binding domain Nuclear inhibitor of protein phosphatase 1 × 1 (Q12972) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 7–307 Fragment:PP1 binding domain Nuclear inhibitor of protein phosphatase 1 × 1 (Q12972) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 7–307 Fragment:PP1 binding domain Nuclear inhibitor of protein phosphatase 1 × 1 (Q12972) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 7–307 Fragment:PP1 binding domain Nuclear inhibitor of protein phosphatase 1 × 1 (Q12972) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

45 other PDB entries and 85 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PP1A_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 6–306; UniProt 7–307 Author chain C; PDBConstruct 6–306; UniProt 7–307 Author chain E; PDBConstruct 6–306; UniProt 7–307 Author chain G; PDBConstruct 6–306; UniProt 7–307

Nuclear inhibitor of protein phosphatase 1

Homo sapiens

UniProt Q12972

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 158–216 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 15P POLYETHYLENE GLYCOL (N=34) × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 158–216 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain F; UniProt 158–216 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196
4 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain H; UniProt 158–216 Not recorded Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.6;277 K;0.08M Bis-Tris, 0.32M KF, 19% PEG1500, pH 6.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.10 Å R-free 0.196

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence
UniProt name PP1R8_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain B; PDBConstruct 4–62; UniProt 158–216 Author chain D; PDBConstruct 4–62; UniProt 158–216 Author chain F; PDBConstruct 4–62; UniProt 158–216 Author chain H; PDBConstruct 4–62; UniProt 158–216

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.

SAXS scattering curve SAXS Profile

SAXS profile for 3v4y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3v4y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3v4y
Deposition date deposition_date2011-12-15
Structure title titleCrystal Structure of the first Nuclear PP1 holoenzyme
Keywords keywordsPP1, Ser/Thr phosphatase, NIPP1, IDP, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier36.04
Radius of gyration Rg (electron density) rg_electron35.05
Forward intensity I(0) i0366951000.00
Molecular weight molecular_weight154910.0 kDa
Excluded volume excluded_volume193460 ų
Envelope volume envelope_volume244380 ų
Hydration-shell volume shell_volume56330 ų
Envelope diameter envelope_diameter113.3
Shell Rg shell_rg43.07
Envelope Rg envelope_rg34.76
Shape Rg shape_rg35.08
Total Rg total_rg35.49
Total atoms total_atoms21465
Residues n_residues1340
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax110.7
Rg (real space) rg_real35.82
Rg uncertainty (real space) rg_real_error0.52
I(0) (real space) i0_real3.6700e+08
I(0) uncertainty (real space) i0_real_error5.3290e+06
Rg (reciprocal space) rg_reciprocal35.96
I(0) (reciprocal space) i0_reciprocal367000000.0000
Solution quality estimate total_estimate0.9016
Solution quality rating solution_quality EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.3
Skewness Skewness skewness0.071
Kurtosis Kurtosis kurtosis-0.593
Angular range angular_range— – 0.2200 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha250900000.0000
Real-space data points n_real_points45
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.937; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.991; Smooth: 0.913

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd3v4ya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd3v4yc1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd3v4yc2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3v4ye_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd3v4yg1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.159 — Metallo-dependent phosphatases
Superfamily Superfamily superfamilyd.159.1 — Metallo-dependent phosphatases
Family Family familyd.159.1.3 — Protein serine/threonine phosphatase
Domain ID domain_idd3v4yg2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (6 domains)

Domain ID domain_id3v4yA00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id3v4yB01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1290
Domain ID domain_id3v4yC00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id3v4yE00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id3v4yG00
Class class3 — Alpha Beta
Architecture architecture60 — 4-Layer Sandwich
Topology topology21 — Purple Acid Phosphatase; chain A, domain 2
Homologous superfamily homologous superfamily10 — Metallo-dependent phosphatases
Domain ID domain_id3v4yH01
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily1290

8. Citations (1)

9. Files and Curves (10)