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7sxi

Solution Structure of Sds3 Capped Tudor Domain

Method: SOLUTION NMR Dmax: 43.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sin3 histone deacetylase corepressor complex component SDS3

Mus musculus

UniProt Q8BR65

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 250–326 Not recorded No other associated polymer SOLUTION NMR NMR measurement conditions：pH 6；298 K；Ionic strength (raw mmCIF value) 0.07；Pressure 1 NMR sample composition：0.35 mM [U-100% 15N] Sds3 CTD, 90% H2O/10% D2O | 90% H2O/10% D2O NMR sample composition：0.35 mM [U-100% 13C; U-100% 15N] Sds3 CTD, 100% D2O | 100% 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 7SXI Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2N2H Solution structure of Sds3 in complex with Sin3A Deposited 2015-05-08 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 205–228（24 aa） Fragment：UNP residues 205-228
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.7；303 K；Ionic strength (raw mmCIF value) 0.12；Pressure ambient
NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sin3HID, 0.5-1 mM Sds3SID, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.5-1 mM [U-100% 13C; U-100% 15N] Sds3SID, 0.5-1 mM Sin3HID, 90% H2O/10% D2O | 90% H2O/10% D2O
Resolution not provided
4ZQA Crystal Structure of the Sds3 Dimerization Domain Deposited 2015-05-08 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 90–172（83 aa） Fragment：UNP residues 90-172
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.4；287 K；15% ethanol (v/v), 200 mM MgCl2, and 100 mM imidazole
Resolution 1.65 Å R-free 0.209

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

View Construct and Data Evidence
UniProt name SDS3_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–79； UniProt 250–326

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 7sxi

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 7sxi
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2. Structure Basics 2. Structure Basics

Entry ID entry_id7sxi
Deposition date deposition_date2021-11-23
Structure title titleSolution Structure of Sds3 Capped Tudor Domain
Keywords keywordsTranscriptional corepressor, Tudor domain, Nucleic acid binding, G-quadruplex binding, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier12.80 Å
Radius of gyration Rg (electron density) rg_electron12.17 Å
Forward intensity I(0) i0509024000.00
Molecular weight molecular_weight187640.0 kDa
Excluded volume excluded_volume234030 ų
Envelope volume envelope_volume21687 ų
Hydration-shell volume shell_volume12943 ų
Envelope diameter envelope_diameter45.4 Å
Shell Rg shell_rg20.03 Å
Envelope Rg envelope_rg14.50 Å
Shape Rg shape_rg12.14 Å
Total Rg total_rg12.44 Å
Total atoms total_atoms26620
Residues n_residues1580
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 dmax43.7 Å
Rg (real space) rg_real12.71 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real5.0900e+08
I(0) uncertainty (real space) i0_real_error5.8410e+06
Rg (reciprocal space) rg_reciprocal12.72 Å
I(0) (reciprocal space) i0_reciprocal509000000.0000
Solution quality estimate total_estimate0.8461
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary17.1 Å
Skewness Skewness skewness0.079
Kurtosis Kurtosis kurtosis-0.283
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha127800.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.668; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.993
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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)