← Back to search
2czy

Solution structure of the NRSF/REST-mSin3B PAH1 complex

Method: SOLUTION NMR Dmax: 41.9 Å Quality: GOOD
▼

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

Paired amphipathic helix protein Sin3b

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 31–107 Fragment：PAH1 domain (residues 31-107) transcription factor REST (version 3) × 1 （Q13127） 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

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 2CZY 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
1PD7 Extended SID of Mad1 bound to the PAH2 domain of mSin3B Deposited 2003-05-19 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 148–232（85 aa） Fragment：PAH2 domain (residues 148-232)
Not recorded No recorded non-water small molecule 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
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
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 1–77； UniProt 31–107

transcription factor REST (version 3)

OrganismNot specified

UniProt Q13127

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 43–57 Fragment：Sin3 interaction domain (residues 43-57) Paired amphipathic helix protein Sin3b × 1 （Q62141） 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

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 Q13127_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–15； UniProt 43–57

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 2czy

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2czy
Download Download
▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id2czy
Deposition date deposition_date2005-07-20
Structure title titleSolution structure of the NRSF/REST-mSin3B PAH1 complex
Keywords keywordsNRSF, Sin3, PAH1, transcriptional repressor, GENE REGULATION; GENE REGULATION
Experimental Method methodSOLUTION NMR
▼

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

Radius of gyration Rg (Guinier) rg_guinier12.90 Å
Radius of gyration Rg (electron density) rg_electron12.46 Å
Forward intensity I(0) i0530588000.00
Molecular weight molecular_weight206800.0 kDa
Excluded volume excluded_volume263390 ų
Envelope volume envelope_volume23254 ų
Hydration-shell volume shell_volume13544 ų
Envelope diameter envelope_diameter48.4 Å
Shell Rg shell_rg20.54 Å
Envelope Rg envelope_rg14.71 Å
Shape Rg shape_rg12.43 Å
Total Rg total_rg12.73 Å
Total atoms total_atoms29440
Residues n_residues1840
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
▼

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

Maximum dimension Dmax dmax41.9 Å
Rg (real space) rg_real12.77 Å
Rg uncertainty (real space) rg_real_error0.29 Å
I(0) (real space) i0_real5.3060e+08
I(0) uncertainty (real space) i0_real_error5.0710e+06
Rg (reciprocal space) rg_reciprocal12.78 Å
I(0) (reciprocal space) i0_reciprocal530600000.0000
Solution quality estimate total_estimate0.7635
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary18.0 Å
Skewness Skewness skewness-0.071
Kurtosis Kurtosis kurtosis-0.310
Angular range angular_range— – 0.5000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha220000.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.655; Stabil: 0.992; Sysdev: 1.000; Positv: 1.000; Valcen: 0.980; Smooth: 0.000
▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

▼

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id2czyA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1160 — Paired amphipathic helix 2 (pah2 repeat)
Homologous superfamily homologous superfamily11 — Paired amphipathic helix
▶

8. Citations (1)

▶

9. Files and Curves (10)