7f3s

Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide

Method: X-RAY DIFFRACTION D_max: 50.4 Å Quality: GOOD

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

Nuclear protein STH1/NPS1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

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 1248–1359	Not recorded	THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LBZ-ALA-PRO-ARG-LYS-GLN-LEU-ALA-SER-TYR × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5；289 K；25% (w/v) PEG 1500, 0.1M MIB/Hydrochloric acid	Resolution 1.40 Å R-free 0.182

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 7F3S	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6K15 RSC substrate-recruitment module Deposited 2019-05-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric	Chain J 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
6KMB Crystal structure of Sth1 bromodomain Deposited 2019-07-31	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1248–1359（112 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M sodium formate, pH 7.0, 20% w/v PEG 3350	Resolution 2.40 Å R-free 0.242
6KMB Crystal structure of Sth1 bromodomain Deposited 2019-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1248–1359（112 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M sodium formate, pH 7.0, 20% w/v PEG 3350	Resolution 2.40 Å R-free 0.242
6KMB Crystal structure of Sth1 bromodomain Deposited 2019-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1248–1359（112 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M sodium formate, pH 7.0, 20% w/v PEG 3350	Resolution 2.40 Å R-free 0.242
6KMB Crystal structure of Sth1 bromodomain Deposited 2019-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1248–1359（112 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2 M sodium formate, pH 7.0, 20% w/v PEG 3350	Resolution 2.40 Å R-free 0.242
6KMJ Crystal structure of Sth1 bromodomain in complex with H3K14Ac Deposited 2019-07-31	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1248–1359（112 aa）	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES sodium pH 7.0, 20% w/v PEG 3350	Resolution 1.40 Å R-free 0.188
6KW3 The ClassA RSC-Nucleosome Complex Deposited 2019-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain J 1–1359（1359 aa） Chain W 1–1359（1359 aa） Chain Y 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.13 Å
6KW4 The ClassB RSC-Nucleosome Complex Deposited 2019-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain J 1–1359（1359 aa） Chain V 1–1359（1359 aa） Chain Y 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.55 Å
6KW5 The ClassC RSC-Nucleosome Complex Deposited 2019-09-06	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 26 PDB declaration: 28-meric	Chain J 1–1359（1359 aa） Chain P 1–1359（1359 aa） Chain Q 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.13 Å
6LQZ Solution structure of Taf14ET-Sth1EBMC Deposited 2020-01-15	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1183–1240（58 aa） Fragment：Sth1EBMC	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 100；Pressure 1 NMR sample composition 1 mM [U-100% 13C; U-100% 15N] Taf14ET, 1.5 mM [U-100% 13C; U-100% 15N] Sth1EBMC, 20 mM Phosphate buffer, 100 mM sodium chloride, 1 % v/v inhabitor cocktail, 0.04 % sodium azide, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 10 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain D 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1250–1359（110 aa） Chain F 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6MR4 Crystal structure of the Sth1 bromodomain from S.cerevisiae Deposited 2018-10-11	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 9 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1250–1359（110 aa） Chain E 1250–1359（110 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2 M magnesium chloride hexahydrate 0.1 M BIS-TRIS pH 6.5 25% (w/v) Polyethylene glycol 3350 3% Trimethylamine N-oxide dihydrate	Resolution 2.71 Å R-free 0.270
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 21 PDB declaration: 23-meric	Chain S 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 15.00 Å
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain G 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6UY1 Crystal structure of the Sth1 bromodomain from Saccharomyces cerevisiae at 2.2 Angstrom resolution Deposited 2019-11-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain H 1250–1359（110 aa） Fragment：bromodomain	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.1 M BIS-TRIS pH 6.5 0.2 M magnesium chloride hexahydrate 25% (w/v) Polyethylene glycol 3350	Resolution 2.21 Å R-free 0.228
6V8O RSC core Deposited 2019-12-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 22 PDB declaration: 22-meric	Chain R 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.07 Å
6V92 RSC-NCP Deposited 2019-12-13	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 33 PDB declaration: 35-meric	Chain R 1–1359（1359 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.9 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 20.00 Å
6VZ4 Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 bound to the nucleosome in ADP Beryllium Fluoride state Deposited 2020-02-27	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric	Chain K 301–1097（797 aa）	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20	Resolution 3.90 Å
6VZG Cryo-EM structure of Sth1-Arp7-Arp9-Rtt102 Deposited 2020-02-28	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 K 301–1097（797 aa）	Not recorded	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE；4 second blot time, blot force 20	Resolution 4.20 Å

14 other PDB entries and 33 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STH1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–112； UniProt 1248–1359

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	7f3s
Deposition date deposition_date	2021-06-17
Structure title title	Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide
Keywords keywords	Histone modification, bromodomain, histone benzoylation, protein-protein interaction, NUCLEAR PROTEIN; NUCLEAR PROTEIN
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	15.81 Å
Radius of gyration Rg (electron density) rg_electron	14.68 Å
Forward intensity I(0) i0	4391950.00
Molecular weight molecular_weight	15093.0 kDa
Excluded volume excluded_volume	18918 Å³
Envelope volume envelope_volume	21489 Å³
Hydration-shell volume shell_volume	12547 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	20.33 Å
Envelope Rg envelope_rg	15.07 Å
Shape Rg shape_rg	14.66 Å
Total Rg total_rg	15.84 Å
Total atoms total_atoms	1065
Residues n_residues	127
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	50.4 Å
Rg (real space) rg_real	15.74 Å
Rg uncertainty (real space) rg_real_error	0.26 Å
I(0) (real space) i0_real	4.3920e+06
I(0) uncertainty (real space) i0_real_error	4.7430e+04
Rg (reciprocal space) rg_reciprocal	15.75 Å
I(0) (reciprocal space) i0_reciprocal	4392000.0000
Solution quality estimate total_estimate	0.8953
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	19.1 Å
Skewness Skewness skewness	0.194
Kurtosis Kurtosis kurtosis	-0.394
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	665300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.987

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Nuclear protein STH1/NPS1
Molecular weight formula_weight	13335.0 kDa
EC 编号 ec_number	3.6.4.12
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	1193

SLGIFPTVEKLVEEMREQLDEVDSHPRTSIFEKLPSKRDYPDYFKVIEKPMAIDIILKNCKNGTYKTLEEVRQALQTMFENARFYNEEGSWVYVDADKLNEFTDEWFKEHSS

来源 Source

来源生物 organism	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
通用名 common_name	;Baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	559292
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	THR-ALA-ARG-LYS-SER-THR-GLY-GLY-LBZ-ALA-PRO-ARG-LYS-GLN-LEU-ALA-SER-TYR
Molecular weight formula_weight	2028.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

TARKSTGGKAPRKQLASY

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	128

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8. Citations (1)

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Unit-cell length a length_a	23.621 Å
Unit-cell length b length_b	33.206 Å
Unit-cell length c length_c	42.449 Å
Unit-cell angle α angle_alpha	88.14 °
Unit-cell angle β angle_beta	83.72 °
Unit-cell angle γ angle_gamma	70.48 °
Molecules per unit cell Z z_pdb	1

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	25.190 Å
R factor r_factor	0.1647
R_work r_work	0.1637
R_free r_free	0.1820

fit	/app/data/saxs_computation/f3/7f3s/7f3s.fit
pddf	/app/data/pr_computation/f3/7f3s/7f3s.pr.out
profile	/app/data/saxs_computation/f3/7f3s/7f3s.dat

Crystal structure of Sth1 Bromodomain in complex with H3K14bz peptide

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

Nuclear protein STH1/NPS1

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

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)