3hvq

Crystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin

Method: X-RAY DIFFRACTION Dmax: 109.8 Å Quality: GOOD

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 7–330 Chain B; UniProt 7–330 Fragment:CATALYTIC SUBUNIT Neurabin-1 × 2 (O35867) MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 7–330 Fragment:CATALYTIC SUBUNIT Neurabin-1 × 1 (O35867) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 7–330 Fragment:CATALYTIC SUBUNIT Neurabin-1 × 1 (O35867) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221

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 86 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 6–329; UniProt 7–330 Author chain B; PDBConstruct 6–329; UniProt 7–330

Neurabin-1

Rattus norvegicus

UniProt O35867

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain C; UniProt 426–592 Chain D; UniProt 426–592 Fragment:PP1 BINDING AND PDZ DOMAINS Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 2 (P62136) MN MANGANESE (II) ION × 4 PO4 PHOSPHATE ION × 2 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 426–592 Fragment:PP1 BINDING AND PDZ DOMAINS Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221
3 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 426–592 Fragment:PP1 BINDING AND PDZ DOMAINS Serine/threonine-protein phosphatase PP1-alpha catalytic subunit × 1 (P62136) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.9;277 K;0.2 M (NH4)2HPO4, 20% PEG 3350, pH 7.9, VAPOR DIFFUSION, SITTING DROP, temperature 277K Resolution 2.20 Å R-free 0.221

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.

2 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEB1_RAT
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 4–170; UniProt 426–592 Author chain D; PDBConstruct 4–170; UniProt 426–592

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 3hvq

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3hvq
Deposition date deposition_date2009-06-16
Structure title titleCrystal structure of a complex between Protein Phosphatase 1 alpha (PP1) and the PP1 binding and PDZ domains of Neurabin
Keywords keywords;PP1, NEURABIN, SERINE/THREONINE PHOSPHATASE, POST SYNAPTIC DENSITY, GLUTAMETERGIC RECEPTORS, CARBOHYDRATE METABOLISM, CELL CYCLE, CELL DIVISION, GLYCOGEN METABOLISM, HYDROLASE, IRON, MANGANESE, METAL-BINDING, PHOSPHOPROTEIN, PROTEIN PHOSPHATASE, ACTIN-BINDING, CELL JUNCTION, CELL PROJECTION, CYTOSKELETON, DEVELOPMENTAL PROTEIN, DIFFERENTIATION, NEUROGENESIS, NUCLEUS, SYNAPSE, Synaptosome, HYDROLASE-HYDROLASE REGULATOR COMPLEX ;; HYDROLASE/HYDROLASE REGULATOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier32.38
Radius of gyration Rg (electron density) rg_electron32.10
Forward intensity I(0) i0131857000.00
Molecular weight molecular_weight91848.0 kDa
Excluded volume excluded_volume114880 ų
Envelope volume envelope_volume140590 ų
Hydration-shell volume shell_volume37410 ų
Envelope diameter envelope_diameter115.1
Shell Rg shell_rg37.83
Envelope Rg envelope_rg32.31
Shape Rg shape_rg32.09
Total Rg total_rg32.57
Total atoms total_atoms6445
Residues n_residues810
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 dmax109.8
Rg (real space) rg_real32.57
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real1.3190e+08
I(0) uncertainty (real space) i0_real_error1.9970e+06
Rg (reciprocal space) rg_reciprocal32.49
I(0) (reciprocal space) i0_reciprocal131800000.0000
Solution quality estimate total_estimate0.8560
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.4
Skewness Skewness skewness0.465
Kurtosis Kurtosis kurtosis-0.341
Angular range angular_range— – 0.2450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha49720000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.802; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.907; Smooth: 0.813

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 5 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3hvqa_
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_idd3hvqb_
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

CATH v4.4 (3 domains)

Domain ID domain_id3hvqA00
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_id3hvqB00
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_id3hvqC01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology42 — Pdz3 Domain
Homologous superfamily homologous superfamily10 — PDZ domain

8. Citations (1)

9. Files and Curves (10)