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6vti

Solution NMR structure of the N-terminal domain of the Serine/threonine-protein phosphatase 1 regulatory subunit 10, PPP1R10

Method: SOLUTION NMR Dmax: 57.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Serine/threonine-protein phosphatase 1 regulatory subunit 10

Rattus norvegicus

UniProt O55000

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–148 Fragment：N-terminal domain residues 1-148 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6.9；303 K；Ionic strength (raw mmCIF value) 200；Pressure 1 NMR sample composition：450 uM [U-13C; U-15N] PPP1R10 N-terminal domain, 2.5 % glycerol, 200 mM NaCl, 20 mM HEPES, 1 mM DTT, 95% H2O/5% D2O | 95% H2O/5% D2O Resolution not provided

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.

Other PDB Difference from Current Entry 6VTI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4MOY Structure of a second nuclear PP1 Holoenzyme, crystal form 1 Deposited 2013-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 393–433（41 aa） Fragment：PP1 Nuclear Targeting Subunit
Not recorded MN MANGANESE (II) ION × 2 CL CHLORIDE ION × 1 PO4 PHOSPHATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；277 K；0.1 M Tris, 1 M LiCl, 18% PEG 6000, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.20 Å R-free 0.185
4MP0 Structure of a second nuclear PP1 Holoenzyme, crystal form 2 Deposited 2013-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 394–433（40 aa） Fragment：PP1 Nuclear Targeting Subunit
Not recorded MN MANGANESE (II) ION × 2 GOL GLYCEROL × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；2% v/v Tacsimate, 0.1 M Tris, 16% w/v Polyethylene glycol 3,350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.202
4MP0 Structure of a second nuclear PP1 Holoenzyme, crystal form 2 Deposited 2013-09-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain D 394–433（40 aa） Fragment：PP1 Nuclear Targeting Subunit
Not recorded MN MANGANESE (II) ION × 2 PO4 PHOSPHATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；2% v/v Tacsimate, 0.1 M Tris, 16% w/v Polyethylene glycol 3,350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Resolution 2.10 Å R-free 0.202
7LQT Solution NMR structure of the PNUTS amino-terminal Domain fused to Myc Homology Box 0 Deposited 2021-02-15 Different construct Different oligomeric state Different experimental conditions Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–148（148 aa）
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.9；303 K；Ionic strength (raw mmCIF value) 200；Pressure 1
NMR sample composition 20 mM HEPES, 200 mM sodium chloride, 2 mM DTT, 5 % glycerol, 400 uM [U-100% 13C; U-100% 15N] labeled protein, 95% H2O/5% D2O | 95% H2O/5% D2O
Resolution not provided
9CI7 Structure of PNUTS:Tox4 complex Deposited 2024-07-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 5–160（156 aa）
Mutation：C48S CL CHLORIDE ION × 4 ZN ZINC ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；298 K；100 mM MES pH 6.5, 1 M LiCl, 15% PEG6K
Resolution 2.10 Å R-free 0.217

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

View Construct and Data Evidence
UniProt name PP1RA_RAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–148； UniProt 1–148

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 6vti

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6vti
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6vti
Deposition date deposition_date2020-02-12
Structure title titleSolution NMR structure of the N-terminal domain of the Serine/threonine-protein phosphatase 1 regulatory subunit 10, PPP1R10
Keywords keywordsPP1-PNUTS phosphatase complex, Regulatory Subunit, c-MYC oncoprotein, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.53 Å
Radius of gyration Rg (electron density) rg_electron15.97 Å
Forward intensity I(0) i01366480000.00
Molecular weight molecular_weight331970.0 kDa
Excluded volume excluded_volume423940 ų
Envelope volume envelope_volume37014 ų
Hydration-shell volume shell_volume17245 ų
Envelope diameter envelope_diameter65.0 Å
Shell Rg shell_rg24.45 Å
Envelope Rg envelope_rg18.88 Å
Shape Rg shape_rg15.92 Å
Total Rg total_rg16.30 Å
Total atoms total_atoms48000
Residues n_residues2960
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax57.8 Å
Rg (real space) rg_real16.52 Å
Rg uncertainty (real space) rg_real_error0.45 Å
I(0) (real space) i0_real1.3660e+09
I(0) uncertainty (real space) i0_real_error1.7180e+07
Rg (reciprocal space) rg_reciprocal16.52 Å
I(0) (reciprocal space) i0_reciprocal1366000000.0000
Solution quality estimate total_estimate0.7543
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary16.5 Å
Skewness Skewness skewness0.297
Kurtosis Kurtosis kurtosis-0.231
Angular range angular_range— – 0.4800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha558000.0000
Real-space data points n_real_points78
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.614; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.960; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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9. Files and Curves (10)