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2r0v

Structure of the Rsc4 tandem bromodomain acetylated at K25

Method: X-RAY DIFFRACTION Dmax: 115.1 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Chromatin structure-remodeling complex protein RSC4

Saccharomyces cerevisiae

UniProt Q02206

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 1–340 Fragment：Rsc4 TBD (1-340) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 3 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；0.1M Tris, 0.2M ammonium sulfate, 22% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K, pH 8.00 Resolution 2.35 Å R-free 0.230
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–340 Fragment：Rsc4 TBD (1-340) Non-standard monomer：Yes (specific site not provided by mmCIF) No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；0.1M Tris, 0.2M ammonium sulfate, 22% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K, pH 8.00 Resolution 2.35 Å R-free 0.230
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–340 Fragment：Rsc4 TBD (1-340) Non-standard monomer：Yes (specific site not provided by mmCIF) SO4 SULFATE ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：pH 8；298 K；0.1M Tris, 0.2M ammonium sulfate, 22% PEG 4000, pH 8.0, VAPOR DIFFUSION, temperature 298K, pH 8.00 Resolution 2.35 Å R-free 0.230

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 2R0V Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2R0S Crystal Structure of the Rsc4 tandem bromodomain Deposited 2007-08-21 Different construct Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 36–320（285 aa） Fragment：Rsc4 tandem 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；pH 4.2；298 K；0.1M phosphate-citrate, 0.2M NaCl, 0.2M ammonium sulfate, 20% PEG 3000, 5% Glycerol, pH 4.2, VAPOR DIFFUSION, temperature 298K
Resolution 1.80 Å R-free 0.218
2R0Y Structure of the Rsc4 tandem bromodomain in complex with an acetylated H3 peptide Deposited 2007-08-21 Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 36–340（305 aa） Fragment：Rsc4 tandem bromodomain (36-340)
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；pH 4.2；298 K；0.1M phosphate-citrate, 0.2M NaCl, 0.2M ammonium sulfate, 20% PEG 3000, 5% Glycerol, pH 4.2, vapor diffusion, temperature 298K
Resolution 1.75 Å R-free 0.219
2R10 Structure of an acetylated Rsc4 tandem bromodomain Histone Chimera Deposited 2007-08-21 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 1–340（340 aa） Fragment：fusion protein comprises Histone H3 (6-18) and Rsc4 TBD (22-361)
Mutation：k9(ALY), K25(ALY) Non-standard monomer：Yes (specific site not provided by mmCIF) EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；298 K；0.1M Tris, 0.2M lithium sulfate, 28% PEG 3000, pH 8.5, VAPOR DIFFUSION, temperature 298K, pH 8.50
Resolution 2.20 Å R-free 0.246
2R10 Structure of an acetylated Rsc4 tandem bromodomain Histone Chimera Deposited 2007-08-21 Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 1–340（340 aa） Fragment：fusion protein comprises Histone H3 (6-18) and Rsc4 TBD (22-361)
Mutation：k9(ALY), K25(ALY) Non-standard monomer：Yes (specific site not provided by mmCIF) No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 8.5；298 K；0.1M Tris, 0.2M lithium sulfate, 28% PEG 3000, pH 8.5, VAPOR DIFFUSION, temperature 298K, pH 8.50
Resolution 2.20 Å R-free 0.246
6K15 RSC substrate-recruitment module Deposited 2019-05-09 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 × 13 PDB declaration: tridecameric
Chain X 1–625（625 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
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 X 1–625（625 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 X 1–625（625 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 X 1–625（625 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
6TDA Structure of SWI/SNF chromatin remodeler RSC bound to a nucleosome Deposited 2019-11-08 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 × 21 PDB declaration: 23-meric
Chain R 1–625（625 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
6V8O RSC core Deposited 2019-12-11 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 × 22 PDB declaration: 22-meric
Chain H 1–625（625 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 mutation/modification 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 H 1–625（625 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

10 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RSC4_YEAST
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 7–346； UniProt 1–340 Author chain B； PDBConstruct 7–346； UniProt 1–340 Author chain C； PDBConstruct 7–346； UniProt 1–340

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 2r0v

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2r0v
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2r0v
Deposition date deposition_date2007-08-21
Structure title titleStructure of the Rsc4 tandem bromodomain acetylated at K25
Keywords keywords;bromodomain, chromatin, remodeler, RSC, histone, acetylation, transcription, Chromatin regulator, Nucleus, Phosphorylation, Transcription regulation ;; TRANSCRIPTION
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.64 Å
Radius of gyration Rg (electron density) rg_electron33.56 Å
Forward intensity I(0) i0151076000.00
Molecular weight molecular_weight103240.0 kDa
Excluded volume excluded_volume131250 ų
Envelope volume envelope_volume174600 ų
Hydration-shell volume shell_volume43836 ų
Envelope diameter envelope_diameter123.3 Å
Shell Rg shell_rg39.96 Å
Envelope Rg envelope_rg33.12 Å
Shape Rg shape_rg33.56 Å
Total Rg total_rg34.11 Å
Total atoms total_atoms7294
Residues n_residues867
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 dmax115.1 Å
Rg (real space) rg_real34.59 Å
Rg uncertainty (real space) rg_real_error1.30 Å
I(0) (real space) i0_real1.5110e+08
I(0) uncertainty (real space) i0_real_error2.7340e+06
Rg (reciprocal space) rg_reciprocal34.62 Å
I(0) (reciprocal space) i0_reciprocal151100000.0000
Solution quality estimate total_estimate0.8987
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary40.0 Å
Skewness Skewness skewness0.252
Kurtosis Kurtosis kurtosis-0.503
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha19990000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.988
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id2r0vA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id2r0vA02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id2r0vB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id2r0vB02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id2r0vC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
Domain ID domain_id2r0vC02
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology920 — Histone Acetyltransferase; Chain A
Homologous superfamily homologous superfamily10 — Bromodomain-like
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8. Citations (1)

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9. Files and Curves (10)