SAXSdb — 2n2h

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

Sin3 histone deacetylase corepressor complex component SDS3

Mus musculus

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 205–228	Fragment：UNP residues 205-228	Paired amphipathic helix protein Sin3a × 1 （Q60520）	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

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 2N2H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
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
7SXI Solution Structure of Sds3 Capped Tudor Domain Deposited 2021-11-23	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 250–326（77 aa）	Not recorded	No recorded non-water small molecule	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

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 4–27； UniProt 205–228

Paired amphipathic helix protein Sin3a

Mus musculus

UniProt Q60520

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 608–729	Fragment：UNP residues 608-729	Sin3 histone deacetylase corepressor complex component SDS3 × 1 （Q8BR65）	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

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 2N2H	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1G1E NMR STRUCTURE OF THE HUMAN MAD1 TRANSREPRESSION DOMAIN SID IN COMPLEX WITH MAMMALIAN SIN3A PAH2 DOMAIN Deposited 2000-10-11	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–383（89 aa） Fragment：PAIRED AMPHIPATHIC HELIX 2 (PAH2 REPEAT)	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM phosphate；Pressure ambient NMR sample composition 1.0 mM 1:1 SID unlabeled, PAH2 U-15N; 1.6 mM 1:1 SID unlabeled, PAH2 U-15N, U-13C. \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN3 \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID unlabeled, PAH2 U-15N,13C; 20 mM phosphate buffer pH 6.0, 0.2% NaN3 \| 100% D2O	Resolution not provided
1S5Q Solution Structure of Mad1 SID-mSin3A PAH2 Complex Deposited 2004-01-21	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–383（89 aa） Fragment：Paired Amphipathic Helix 2, (PAH2 repeat), Residues 295 to 383	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6, 0.2% NaN3；Pressure ambient NMR sample composition 1.0 mM 1:1 SID UNLABELED, PAH2 U-15N \| 90% H2O/10% D2O NMR sample composition 1.6 mM 1:1 SID UNLABELED, PAH2 U-15N,U-13C \| 100% D2O	Resolution not provided
1S5R Solution Structure of HBP1 SID-mSin3A PAH2 Complex Deposited 2004-01-21	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–383（89 aa） Fragment：Paired Amphipathic Helix 2, (PAH2 repeat), Residues 295 to 383	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；300 K；Ionic strength (raw mmCIF value) 20 mM sodium phosphate, pH 6, 0.2% NaN3；Pressure ambient NMR sample composition 1.1 mM 1:1 SID UNLABELED, PAH2 U-15N \| 90% H2O/10% D2O NMR sample composition 1.4 mM 1:1 SID UNLABELED, PAH2 U-15N,13C \| 100% D2O	Resolution not provided
2L9S Solution structure of Pf1 SID1-mSin3A PAH2 Complex Deposited 2011-02-23	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 295–385（91 aa） Fragment：PAH 2 domain residues 295-385	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0；Pressure ambient NMR sample composition 0.75-1.5 mM [U-100% 13C; U-100% 15N] peptide, 0.75-1.5 mM [U-100% 13C; U-100% 15N] protein, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2LD7 Solution structure of the mSin3A PAH3-SAP30 SID complex Deposited 2011-05-16	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 456–528（73 aa） Fragment：PAH 3 domain residues 456-528	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；308 K NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 1 mM [U-100% 13C; U-100% 15N] protein 1, 1 mM protein 2, 100% D2O \| 100% D2O NMR sample composition 1 mM protein 1, 1 mM [U-100% 13C; U-100% 15N] protein 2, 100% D2O \| 100% D2O	Resolution not provided
2RMR Solution structure of mSin3A PAH1 domain Deposited 2007-11-14	Different construct Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 119–189（71 aa） Fragment：UNP residues 119-189	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；288 K；Ionic strength (raw mmCIF value) .02；Pressure ambient NMR sample composition 0.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.7-1.0mM [U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM [U-13C; U-15N] Sin3A PAH1 domain, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RMS Solution structure of the mSin3A PAH1-SAP25 SID complex Deposited 2007-11-14	Different construct Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 119–189（71 aa） Fragment：UNP residues 119-189	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；303 K；Ionic strength (raw mmCIF value) .02；Pressure ambient NMR sample composition 0.7-1.0mM [U-15N] SIN3A, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM SIN3A, 0.7-1.0mM [U-15N] SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.7-1.0mM [U-13C; U-15N] SIN3A, 0.7-1.0mM SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O NMR sample composition 0.7-1.0mM SIN3A , 0.7-1.0mM [U-13C; U-15N] SAP25, 20mM sodium phosphate, 2mM DTT, 0.2% sodium azide, 100% D2O \| 100% D2O	Resolution not provided

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SIN3A_MOUSE
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 4–125； UniProt 608–729

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	2n2h
Deposition date deposition_date	2015-05-08
Structure title title	Solution structure of Sds3 in complex with Sin3A
Keywords keywords	transcription repression, corepressor complex, histone deacetylase complex, Transcription, protein binding; Transcription, protein binding
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	19.23 Å
Radius of gyration Rg (electron density) rg_electron	19.01 Å
Forward intensity I(0) i0	1780890000.00
Molecular weight molecular_weight	355950.0 kDa
Excluded volume excluded_volume	445940 Å³
Envelope volume envelope_volume	65652 Å³
Hydration-shell volume shell_volume	23216 Å³
Envelope diameter envelope_diameter	80.3 Å
Shell Rg shell_rg	30.80 Å
Envelope Rg envelope_rg	25.67 Å
Shape Rg shape_rg	19.01 Å
Total Rg total_rg	19.23 Å
Total atoms total_atoms	50740
Residues n_residues	3040
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	74.2 Å
Rg (real space) rg_real	19.47 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	1.7810e+09
I(0) uncertainty (real space) i0_real_error	2.5980e+07
Rg (reciprocal space) rg_reciprocal	19.43 Å
I(0) (reciprocal space) i0_reciprocal	1781000000.0000
Solution quality estimate total_estimate	0.7486
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	18.6 Å
Skewness Skewness skewness	0.654
Kurtosis Kurtosis kurtosis	0.102
Angular range angular_range	— – 0.4150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	982500.0000
Real-space data points n_real_points	73
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.437; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.422; Smooth: 0.994

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Sin3 histone deacetylase corepressor complex component SDS3
Molecular weight formula_weight	3125.5 kDa
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	50740

SNAAQLNYLLTDEQIMEDLRTLNKLKS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Paired amphipathic helix protein Sin3a
Molecular weight formula_weight	14698.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

SNAEHIYRCEDERFELDVVLETNLATIRVLEAIQKKLSRLSAEEQAKFRLDNTLGGTSEVIHRKALQRIYADKAADIIDGLRKNPSIAVPIVLKRLKMKEEEWREAQRGFNKVWREQNEKYYLKS

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

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8. Citations (1)

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fit	/app/data/saxs_computation/n2/2n2h/2n2h.fit
pddf	/app/data/pr_computation/n2/2n2h/2n2h.pr.out
profile	/app/data/saxs_computation/n2/2n2h/2n2h.dat

Solution structure of Sds3 in complex with Sin3A

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

Sin3 histone deacetylase corepressor complex component SDS3

State in the Current Structure

Other States of the Same Protein in the Database

Paired amphipathic helix protein Sin3a

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

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)