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2l9s

Solution structure of Pf1 SID1-mSin3A PAH2 Complex

Method: SOLUTION NMR Dmax: 75.6 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

PHD finger protein 12

Homo sapiens

UniProt Q96QT6

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 200–241 Fragment：sequence database residues 200-241 Paired amphipathic helix protein Sin3a × 1 （Q60520） 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

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 2L9S Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2LKM Structural Basis for Molecular Interactions Involving MRG Domains: Implications in Chromatin Biology Deposited 2011-10-16 Different construct Different experimental conditions Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 200–241（42 aa） Fragment：UNP residues 200-241
Not recorded No recorded non-water small molecule SOLUTION NMR
NMR measurement conditions pH 6.8；298 K
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM [U-100% 13C; U-100% 15N] protein_1, 0.9 mM protein_2, 50 mM potassium chloride, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% D2O
NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 10 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition 0.9 mM protein_1, 0.9 mM [U-100% 13C; U-100% 15N] protein_2, 50 mM sodium phosphate, 100 % [U-100% 2H] D2O, 5 mM [U-2H] DTT, 0.2 % sodium azide, 100% D2O | 100% D2O
Resolution not provided
8BPA Cryo-EM structure of the human SIN3B histone deacetylase complex at 3.7 Angstrom Deposited 2022-11-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1004（1004 aa）
Not recorded ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
8BPB Cryo-EM structure of the human SIN3B histone deacetylase core complex at 2.8 Angstrom Deposited 2022-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–256（256 aa）
Chain C 257–364（108 aa）
Not recorded ZN ZINC ION × 3 CA CALCIUM ION × 2 ACT ACETATE ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8BPC Cryo-EM structure of the human SIN3B histone deacetylase core complex with SAHA at 2.8 Angstrom Deposited 2022-11-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain C 1–256（256 aa）
Chain C 257–364（108 aa）
Not recorded SHH OCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE × 1 ZN ZINC ION × 3 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.80 Å
8C60 Cryo-EM structure of the human SIN3B full-length complex at 3.4 Angstrom resolution Deposited 2023-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain C 1–1004（1004 aa）
Not recorded ZN ZINC ION × 5 CA CALCIUM ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å

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

View Construct and Data Evidence
UniProt name PHF12_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–45； UniProt 200–241

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 295–385 Fragment：PAH 2 domain residues 295-385 PHD finger protein 12 × 1 （Q96QT6） 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

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 2L9S 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
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 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 4–94； UniProt 295–385

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 2l9s

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2l9s
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2l9s
Deposition date deposition_date2011-02-23
Structure title titleSolution structure of Pf1 SID1-mSin3A PAH2 Complex
Keywords keywordsProtein-Peptide Complex, Amphipathic Helix motif, 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_guinier18.07 Å
Radius of gyration Rg (electron density) rg_electron17.09 Å
Forward intensity I(0) i01465530000.00
Molecular weight molecular_weight315870.0 kDa
Excluded volume excluded_volume391960 ų
Envelope volume envelope_volume84084 ų
Hydration-shell volume shell_volume28899 ų
Envelope diameter envelope_diameter85.3 Å
Shell Rg shell_rg31.65 Å
Envelope Rg envelope_rg24.70 Å
Shape Rg shape_rg17.03 Å
Total Rg total_rg17.65 Å
Total atoms total_atoms43920
Residues n_residues2780
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 dmax75.6 Å
Rg (real space) rg_real18.10 Å
Rg uncertainty (real space) rg_real_error0.73 Å
I(0) (real space) i0_real1.4660e+09
I(0) uncertainty (real space) i0_real_error1.9530e+07
Rg (reciprocal space) rg_reciprocal18.09 Å
I(0) (reciprocal space) i0_reciprocal1466000000.0000
Solution quality estimate total_estimate0.7426
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary20.4 Å
Skewness Skewness skewness0.465
Kurtosis Kurtosis kurtosis0.247
Angular range angular_range— – 0.4400 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha948200.0000
Real-space data points n_real_points75
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.318; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.697; Smooth: 1.000
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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) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd2l9sb1
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
Domain ID domain_idd2l9sb2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (2 domains)

Domain ID domain_id2l9sA00
Class class6 — Special
Architecture architecture10 — Helix non-globular
Topology topology20 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily60 — PHD finger protein 12
Domain ID domain_id2l9sB00
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)