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2rms

Solution structure of the mSin3A PAH1-SAP25 SID complex

Method: SOLUTION NMR Dmax: 81.3 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 A； UniProt 119–189 Fragment：UNP residues 119-189 MSin3A-binding protein × 1 （Q1EHW4） 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

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 2RMS 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
2N2H Solution structure of Sds3 in complex with Sin3A Deposited 2015-05-08 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 608–729（122 aa） Fragment：UNP residues 608-729
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
2RMR Solution structure of mSin3A PAH1 domain Deposited 2007-11-14 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

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 1
Chains and sequence ranges Author chain A； PDBConstruct 1–71； UniProt 119–189

MSin3A-binding protein

Mus musculus

UniProt Q1EHW4

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 126–186 Fragment：UNP residues 126-186 Paired amphipathic helix protein Sin3a × 1 （Q60520） 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

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 Q1EHW4_MOUSE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–61； UniProt 126–186

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 2rms

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2rms
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2rms
Deposition date deposition_date2007-11-14
Structure title titleSolution structure of the mSin3A PAH1-SAP25 SID complex
Keywords keywordsProtein/Protein interaction, PAH domain, SIN3 corepressor, Transcription repression, Transcription regulation, 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_guinier20.74 Å
Radius of gyration Rg (electron density) rg_electron19.59 Å
Forward intensity I(0) i01212130000.00
Molecular weight molecular_weight284220.0 kDa
Excluded volume excluded_volume351940 ų
Envelope volume envelope_volume123030 ų
Hydration-shell volume shell_volume34984 ų
Envelope diameter envelope_diameter91.1 Å
Shell Rg shell_rg36.43 Å
Envelope Rg envelope_rg30.48 Å
Shape Rg shape_rg19.59 Å
Total Rg total_rg20.15 Å
Total atoms total_atoms39180
Residues n_residues2640
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 dmax81.3 Å
Rg (real space) rg_real21.05 Å
Rg uncertainty (real space) rg_real_error0.90 Å
I(0) (real space) i0_real1.2120e+09
I(0) uncertainty (real space) i0_real_error1.6470e+07
Rg (reciprocal space) rg_reciprocal20.99 Å
I(0) (reciprocal space) i0_reciprocal1212000000.0000
Solution quality estimate total_estimate0.7001
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.9 Å
Skewness Skewness skewness0.695
Kurtosis Kurtosis kurtosis0.079
Angular range angular_range— – 0.3850 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha1836000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.276; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.273; Smooth: 0.995
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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) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd2rmsa_
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 (2 domains)

Domain ID domain_id2rmsA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1160 — Paired amphipathic helix 2 (pah2 repeat)
Homologous superfamily homologous superfamily11 — Paired amphipathic helix
Domain ID domain_id2rmsB00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology140 — Helix Hairpins
Homologous superfamily homologous superfamily710 —
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8. Citations (1)

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9. Files and Curves (10)