SAXSdb — 9ci7

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

Serine/threonine-protein phosphatase 1 regulatory subunit 10

Rattus norvegicus

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 5–160	Mutation：C48S	TOX high mobility group box family member 4 × 1 （O94842） 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

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 9CI7	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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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
6VTI Solution NMR structure of the N-terminal domain of the Serine/threonine-protein phosphatase 1 regulatory subunit 10, PPP1R10 Deposited 2020-02-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–148（148 aa） Fragment：N-terminal domain residues 1-148	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 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
7LQT Solution NMR structure of the PNUTS amino-terminal Domain fused to Myc Homology Box 0 Deposited 2021-02-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	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

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 4–159； UniProt 5–160

TOX high mobility group box family member 4

Homo sapiens

UniProt O94842

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 571–621	Mutation：C601S	Serine/threonine-protein phosphatase 1 regulatory subunit 10 × 1 （O55000） 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

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	TOX4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–54； UniProt 571–621

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	9ci7
Deposition date deposition_date	2024-07-02
最后修订 last_revision	2025-05-21
Structure title title	Structure of PNUTS:Tox4 complex
Keywords keywords	;PNUTS, PPP1R10, Transcriptional elongation factor S-II homology N-terminal domain. Tox4, zinc binding protein, complex, SIGNALING PROTEIN ;; SIGNALING PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	18.81 Å
Radius of gyration Rg (electron density) rg_electron	17.61 Å
Forward intensity I(0) i0	9500960.00
Molecular weight molecular_weight	22826.0 kDa
Excluded volume excluded_volume	28644 Å³
Envelope volume envelope_volume	33909 Å³
Hydration-shell volume shell_volume	16384 Å³
Envelope diameter envelope_diameter	63.5 Å
Shell Rg shell_rg	23.57 Å
Envelope Rg envelope_rg	18.13 Å
Shape Rg shape_rg	17.56 Å
Total Rg total_rg	18.73 Å
Total atoms total_atoms	1588
Residues n_residues	199
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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

Maximum dimension Dmax dmax	67.9 Å
Rg (real space) rg_real	18.74 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	9.5010e+06
I(0) uncertainty (real space) i0_real_error	1.1070e+05
Rg (reciprocal space) rg_reciprocal	18.75 Å
I(0) (reciprocal space) i0_reciprocal	9501000.0000
Solution quality estimate total_estimate	0.7715
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	23.3 Å
Skewness Skewness skewness	0.228
Kurtosis Kurtosis kurtosis	-0.297
Angular range angular_range	— – 0.4250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1604000.0000
Real-space data points n_real_points	74
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.687; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Serine/threonine-protein phosphatase 1 regulatory subunit 10
Molecular weight formula_weight	18029.0 kDa
Mutation mutation	C48S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1735

GHMPIDPKELLKGLDSFLTRDGEVKSVDGIAKIFSLMKEARKMVSRSTYLNIILQTRAPEVLVKFIDVGGYKLLNSWLTYSKTTNNIPLLQQILLTLQHLPLTVDHLKQNNTAKLVKQLSKSSEDEELRKLASVLVSDWMAVIRSQSSTQPAEKDKKKR

来源 Source

来源生物 organism	Rattus norvegicus
通用名 common_name	Norway rat
NCBI Class编号 ncbi_taxonomy_id	10116
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	TOX high mobility group box family member 4
Molecular weight formula_weight	6180.0 kDa
Mutation mutation	C601S
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GHMRCVRSGCENPPIVSKDWDNEYCSNECVVKHSRDVFLAWVASRNSNTVVFVK

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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8. Citations (1)

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Unit-cell length a length_a	70.630 Å
Unit-cell length b length_b	70.630 Å
Unit-cell length c length_c	97.165 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 61
Space-group number int_tables_number	169
Crystal system crystal_system	hexagonal

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	35.320 Å
R factor r_factor	0.1896
R_work r_work	0.1882
R_free r_free	0.2167

fit	/app/data/saxs_computation/ci/9ci7/9ci7.fit
pddf	/app/data/pr_computation/ci/9ci7/9ci7.pr.out
profile	/app/data/saxs_computation/ci/9ci7/9ci7.dat

Structure of PNUTS:Tox4 complex

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

Serine/threonine-protein phosphatase 1 regulatory subunit 10

State in the Current Structure

Other States of the Same Protein in the Database

TOX high mobility group box family member 4

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

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

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)