6zeh

Structure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580)

Method: X-RAY DIFFRACTION Dmax: 99.2 Å Quality: GOOD

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

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1

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 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 7–304 Mutation:N-terminal Vector derived sequence GHMGS Phosphatase and actin regulator × 1 (Q4VY12) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 7–304 Mutation:N-terminal Vector derived sequence GHMGS Phosphatase and actin regulator × 1 (Q4VY12) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169

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 87 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 6–303; UniProt 7–304 Author chain B; PDBConstruct 6–303; UniProt 7–304

Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1

Homo sapiens

UniProt Q13813

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1025–1039 Mutation:N-terminal Vector derived sequence GHMGS Phosphatase and actin regulator × 1 (Q4VY12) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 1025–1039 Mutation:N-terminal Vector derived sequence GHMGS Phosphatase and actin regulator × 1 (Q4VY12) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169

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.

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SPTN1_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 322–336; UniProt 1025–1039 Author chain B; PDBConstruct 322–336; UniProt 1025–1039

Phosphatase and actin regulator

Homo sapiens

UniProt Q4VY12

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 80–144 Mutation:N-terminal Vector derived sequence GPLGS Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1 × 1 (P62136,Q13813) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169
2 Insufficient information Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 80–144 Mutation:N-terminal Vector derived sequence GPLGS Serine/threonine-protein phosphatase PP1-alpha catalytic subunit,Spectrin alpha chain, non-erythrocytic 1 × 1 (P62136,Q13813) MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 SO4 SULFATE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 8.5;293 K;20% (w/v) polyethylene glycol 3350, 0.2 M NaI and 0.1 M BIS-Tris propane pH 8.5 Resolution 1.30 Å R-free 0.169

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.

5 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q4VY12_HUMAN
Isoform
PDB entities 2
Chains and sequence ranges Author chain C; PDBConstruct 6–70; UniProt 80–144 Author chain D; PDBConstruct 6–70; UniProt 80–144

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 6zeh

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6zeh
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id6zeh
Deposition date deposition_date2020-06-16
Structure title titleStructure of PP1-spectrin alpha II chimera [PP1(7-304) + linker (G/S)x9 + spectrin alpha II (1025-1039)] bound to Phactr1 (516-580)
Keywords keywordsPP1, Phosphatase, Phactr, RPEL, HYDROLASE; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier30.59
Radius of gyration Rg (electron density) rg_electron29.69
Forward intensity I(0) i0117051000.00
Molecular weight molecular_weight85107.0 kDa
Excluded volume excluded_volume106110 ų
Envelope volume envelope_volume125750 ų
Hydration-shell volume shell_volume35317 ų
Envelope diameter envelope_diameter104.5
Shell Rg shell_rg36.71
Envelope Rg envelope_rg29.83
Shape Rg shape_rg29.71
Total Rg total_rg30.25
Total atoms total_atoms11772
Residues n_residues742
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 dmax99.2
Rg (real space) rg_real30.67
Rg uncertainty (real space) rg_real_error0.57
I(0) (real space) i0_real1.1710e+08
I(0) uncertainty (real space) i0_real_error1.6700e+06
Rg (reciprocal space) rg_reciprocal30.64
I(0) (reciprocal space) i0_reciprocal117000000.0000
Solution quality estimate total_estimate0.8757
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary30.5
Skewness Skewness skewness0.372
Kurtosis Kurtosis kurtosis-0.569
Angular range angular_range— – 0.2600 −1
Current regularization parameter α current_alpha0.0001
Highest regularization parameter α highest_alpha50690000.0000
Real-space data points n_real_points53
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.855; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.936; Smooth: 0.878

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6zehA01
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_id6zehB01
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

8. Citations (1)

9. Files and Curves (10)