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1pd7

Extended SID of Mad1 bound to the PAH2 domain of mSin3B

Method: SOLUTION NMR Dmax: 52.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Sin3b protein

Mus musculus

UniProt Q62141

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 148–232 Fragment：PAH2 domain (residues 148-232) Mad1 × 1 （Q05195） SOLUTION NMR NMR measurement conditions：pH 6.3；293 K；Ionic strength (raw mmCIF value) 50 mM K2HPO4/KH2PO4；Pressure ambient NMR sample composition：1.3 mM PAH2 U-15,13C; 1.3 mM SID 50 mM phosphate buffer pH 6.3 trace amounts of NaN3 and Pefabloc | 95% H20, 5% D20 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 1PD7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E91 Structure of the complex of the Mad1-Sin3B interaction domains Deposited 2000-10-04 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 148–232（85 aa） Fragment：PAH2 DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；293 K
Resolution not provided
2CR7 Solution structure of the first PAH domain of the mouse transcriptional repressor SIN3B Deposited 2005-05-20 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–98（67 aa） Fragment：PAH
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition 1.28mM 13C,15N-labeled protein | 20mM d-Tris-HCl(pH7.0); 100mM NaCl; 1mM d-DTT; 0.02%NaN3; 90% H2O; 10% D2O
Resolution not provided
2CZY Solution structure of the NRSF/REST-mSin3B PAH1 complex Deposited 2005-07-20 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 31–107（77 aa） Fragment：PAH1 domain (residues 31-107)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 7.5；293 K；Ionic strength (raw mmCIF value) 20mM potassium phosphate；Pressure ambient
NMR sample composition 0.5-0.8mM PAH1 U-15N,13C; 0.5-0.8mM SID; 20mM potassium phosphate buffer | 95% H2O/5% D2O
NMR sample composition 0.5-0.8mM PAH1 U-15N,13C; 0.5-0.8mM SID; 20mM potassium phosphate buffer | 100% D2O
Resolution not provided
2F05 Solution structure of free PAH2 domain of mSin3B Deposited 2005-11-11 Different construct Different oligomeric state Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 148–252（105 aa） Fragment：PAH2 domain (residues 148-252)
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；293 K；Ionic strength (raw mmCIF value) 150；Pressure 1
NMR sample composition 0.9 mM PAH2 uniform 13C/15N labeled, H2O, 100mM KCl, 50 mM Pi buffer pH 6.3 | H2O, 100mM KCl, 50 mM Pi buffer pH 6.3
Resolution not provided
5Y95 Haddock model of mSIN3B PAH1 domain Deposited 2017-08-22 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 32–98（67 aa） Fragment：UNP RESIDUES 32-98
Not recorded 8TL propan-2-yl (3R,6S,9aS)-3-ethyl-8-(3-methylbutyl)-6-(2-methylsulfanylethyl)-4,7-bis(oxidanylidene)-9,9a-dihydro-6H-pyrazino[2,1-c][1,2,4]oxadiazine-1-carboxylate × 1 SOLUTION NMR
NMR measurement conditions pH 7.2；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1
NMR sample composition 100 uM [U-99% 15N] mSin3B, 100 mM sodium phosphate, 95% H2O/5% DMSO | 95% H2O/5% DMSO
Resolution not provided

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

View Construct and Data Evidence
UniProt name SIN3B_MOUSE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–85； UniProt 148–232

Mad1

OrganismNot specified

UniProt Q05195

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 5–28 Fragment：extended SID domain (residues 5-28) Sin3b protein × 1 （Q62141） SOLUTION NMR NMR measurement conditions：pH 6.3；293 K；Ionic strength (raw mmCIF value) 50 mM K2HPO4/KH2PO4；Pressure ambient NMR sample composition：1.3 mM PAH2 U-15,13C; 1.3 mM SID 50 mM phosphate buffer pH 6.3 trace amounts of NaN3 and Pefabloc | 95% H20, 5% D20 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 1PD7 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1E91 Structure of the complex of the Mad1-Sin3B interaction domains Deposited 2000-10-04 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 8–20（13 aa） Fragment：SIN INTERACTION DOMAIN
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.3；293 K
Resolution not provided
1NLW Crystal structure of Mad-Max recognizing DNA Deposited 2003-01-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain A 57–136（80 aa） Fragment：bHLHZ region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；20% MPD, 5mM magnesium chloride, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.00 Å R-free 0.324
1NLW Crystal structure of Mad-Max recognizing DNA Deposited 2003-01-07 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 2 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain D 57–136（80 aa） Fragment：bHLHZ region
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；288 K；20% MPD, 5mM magnesium chloride, 50 mM sodium cacodylate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K
Resolution 2.00 Å R-free 0.324
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 A 6–21（16 aa） Fragment：Sin3 Interaction Domain (SID), Residues 6 to 21
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

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

View Construct and Data Evidence
UniProt name MAD_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–24； UniProt 5–28

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 1pd7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1pd7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1pd7
Deposition date deposition_date2003-05-19
Structure title titleExtended SID of Mad1 bound to the PAH2 domain of mSin3B
Keywords keywordsPAH2, SIN3, MAD1, EUKARYOTIC TRANSCRIPTIONAL REGULATION, PROTEIN-PROTEIN INTERACTIONS, TRANSCRIPTION; TRANSCRIPTION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier15.58 Å
Radius of gyration Rg (electron density) rg_electron14.79 Å
Forward intensity I(0) i02211860000.00
Molecular weight molecular_weight391520.0 kDa
Excluded volume excluded_volume486030 ų
Envelope volume envelope_volume42897 ų
Hydration-shell volume shell_volume19289 ų
Envelope diameter envelope_diameter60.8 Å
Shell Rg shell_rg24.96 Å
Envelope Rg envelope_rg18.94 Å
Shape Rg shape_rg14.77 Å
Total Rg total_rg15.01 Å
Total atoms total_atoms54510
Residues n_residues3270
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 dmax52.8 Å
Rg (real space) rg_real15.52 Å
Rg uncertainty (real space) rg_real_error0.37 Å
I(0) (real space) i0_real2.2120e+09
I(0) uncertainty (real space) i0_real_error2.6280e+07
Rg (reciprocal space) rg_reciprocal15.52 Å
I(0) (reciprocal space) i0_reciprocal2212000000.0000
Solution quality estimate total_estimate0.7858
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.1 Å
Skewness Skewness skewness0.220
Kurtosis Kurtosis kurtosis-0.232
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha353300.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.739; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd1pd7a_
Class classa — All alpha proteins
Fold Fold folda.59 — PAH2 domain
Superfamily Superfamily superfamilya.59.1 — PAH2 domain
Family Family familya.59.1.1 — PAH2 domain

CATH v4.4 (1 domains)

Domain ID domain_id1pd7A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1160 — Paired amphipathic helix 2 (pah2 repeat)
Homologous superfamily homologous superfamily11 — Paired amphipathic helix
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8. Citations (1)

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9. Files and Curves (10)