SAXSdb — 8i3f

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

Chromatin modification-related protein EAF3

Saccharomyces cerevisiae

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 218–400	Not recorded	RCO1 isoform 1 × 1 （A0A8H4BXB0） Histone H3 × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M MgCl2, 0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.2 M NDSB-201	Resolution 1.62 Å R-free 0.188

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 8I3F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HXX Cryo-EM structure of the histone deacetylase complex Rpd3S Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain M 1–401（401 aa） Chain O 1–401（401 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 13 PDB declaration: pentadecameric	Chain M 1–401（401 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8HXZ Cryo-EM structure of Eaf3 CHD in complex with nucleosome Deposited 2023-01-05	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain M 1–401（401 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.40 Å
8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	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 × 14 PDB declaration: hexadecameric	Chain M 1–401（401 aa） Chain O 1–401（401 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8I3G Crystal structure of Eaf3-Eaf7 complex Deposited 2023-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–401（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.025% v/v Dichloromethane	Resolution 2.40 Å R-free 0.256
8I3G Crystal structure of Eaf3-Eaf7 complex Deposited 2023-01-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 218–401（184 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.025% v/v Dichloromethane	Resolution 2.40 Å R-free 0.256
8IHM Eaf3 CHD domain bound to the nucleosome Deposited 2023-02-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain N 13–131（119 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
8IHN Cryo-EM structure of the Rpd3S core complex Deposited 2023-02-23	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 × 7 PDB declaration: heptameric	Chain N 1–401（401 aa） Chain P 1–401（401 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23	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 × 14 PDB declaration: hexadecameric	Chain N 1–401（401 aa） Chain P 1–401（401 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25	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 × 22 PDB declaration: 24-meric	Chain M 1–401（401 aa） Chain O 1–401（401 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å

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

View Construct and Data Evidence

UniProt name	A0A8H4F719_YEASX
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–183； UniProt 218–400

RCO1 isoform 1

Saccharomyces cerevisiae

UniProt A0A8H4BXB0

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain B； UniProt 258–375	Not recorded	Chromatin modification-related protein EAF3 × 1 （A0A8H4F719） Histone H3 × 1 ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M MgCl2, 0.1 M tris pH 8.5, 25% w/v PEG 4000, 0.2 M NDSB-201	Resolution 1.62 Å R-free 0.188

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 8I3F	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8HXX Cryo-EM structure of the histone deacetylase complex Rpd3S Deposited 2023-01-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain N 1–684（684 aa） Chain P 1–684（684 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
8HXY Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	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 × 13 PDB declaration: pentadecameric	Chain N 1–684（684 aa） Chain P 1–684（684 aa）	Not recorded	ZN ZINC ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8HY0 Composite cryo-EM structure of the histone deacetylase complex Rpd3S in complex with nucleosome Deposited 2023-01-05	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 × 14 PDB declaration: hexadecameric	Chain N 1–684（684 aa） Chain P 1–684（684 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.10 Å
8IHN Cryo-EM structure of the Rpd3S core complex Deposited 2023-02-23	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 × 7 PDB declaration: heptameric	Chain M 1–684（684 aa） Chain O 1–684（684 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.37 Å
8IHT Rpd3S bound to the nucleosome Deposited 2023-02-23	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 × 14 PDB declaration: hexadecameric	Chain M 1–684（684 aa） Chain O 1–684（684 aa）	Not recorded	ZN ZINC ION × 1 CA CALCIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.72 Å
8JHO Cryo-EM structure of the histone deacetylase complex Rpd3S in complex with di-nucleosome Deposited 2023-05-25	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 × 22 PDB declaration: 24-meric	Chain N 1–684（684 aa） Chain P 1–684（684 aa）	Not recorded	ZN ZINC ION × 7	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20 mM HEPES-Na pH 7.5, 40 mM KCl, 2 mM MgCl2, 1 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 7.60 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	A0A8H4BXB0_YEASX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–118； UniProt 258–375

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8i3f
Deposition date deposition_date	2023-01-17
Structure title title	Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal
Keywords keywords	MRG domain, complex, PHD domain, STRUCTURAL PROTEIN; STRUCTURAL 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	21.13 Å
Radius of gyration Rg (electron density) rg_electron	19.68 Å
Forward intensity I(0) i0	20069400.00
Molecular weight molecular_weight	34452.0 kDa
Excluded volume excluded_volume	43253 Å³
Envelope volume envelope_volume	50373 Å³
Hydration-shell volume shell_volume	21204 Å³
Envelope diameter envelope_diameter	66.5 Å
Shell Rg shell_rg	26.29 Å
Envelope Rg envelope_rg	19.92 Å
Shape Rg shape_rg	19.68 Å
Total Rg total_rg	20.59 Å
Total atoms total_atoms	2419
Residues n_residues	307
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	65.5 Å
Rg (real space) rg_real	20.99 Å
Rg uncertainty (real space) rg_real_error	0.41 Å
I(0) (real space) i0_real	2.0070e+07
I(0) uncertainty (real space) i0_real_error	2.7710e+05
Rg (reciprocal space) rg_reciprocal	21.02 Å
I(0) (reciprocal space) i0_reciprocal	20070000.0000
Solution quality estimate total_estimate	0.9050
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.123
Kurtosis Kurtosis kurtosis	-0.473
Angular range angular_range	— – 0.3750 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3035000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.923; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.994; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Chromatin modification-related protein EAF3
Molecular weight formula_weight	21127.4 kDa
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	2737

PKISLQIPIKLKSVLVDDWEYVTKDKKICRLPADVTVEMVLNKYEHEVSQELESPGSQSQLSEYCAGLKLYFDKCLGNMLLYRLERLQYDELLKKSSKDQKPLVPIRIYGAIHLLRLISVLPELISSTTMDLQSCQLLIKQTEDFLVWLLMHVDEYFNDKDPNRSDDALYVNTSSQYEGVALG

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	RCO1 isoform 1
Molecular weight formula_weight	13532.3 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ENEDFCSACNQSGSFLCCDTCPKSFHFLCLDPPIDPNNLPKGDWHCNECKFKIFINNSMATLKKIESNFIKQNNNVKIFAKLLFNIDSHNPKQFQLPNYIKETFPAVKTGSRGQYSDE

来源 Source

来源生物 organism	Saccharomyces cerevisiae
通用名 common_name	;baker's yeast ;
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	Histone H3
Molecular weight formula_weight	705.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

ARTKQT

来源 Source

来源生物 organism	Saccharomyces cerevisiae
NCBI Class编号 ncbi_taxonomy_id	4932
宿主生物 host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	295

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8. Citations (1)

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Unit-cell length a length_a	82.513 Å
Unit-cell length b length_b	75.546 Å
Unit-cell length c length_c	73.421 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	114.19 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.620 Å
Low-resolution limit resolution_low	28.237 Å
R factor r_factor	0.1684
R_work r_work	0.1674
R_free r_free	0.1879

fit	/app/data/saxs_computation/i3/8i3f/8i3f.fit
pddf	/app/data/pr_computation/i3/8i3f/8i3f.pr.out
profile	/app/data/saxs_computation/i3/8i3f/8i3f.dat

Crystal structure of Rco1-Eaf3 with peptide of histone H3 N-terminal

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

Chromatin modification-related protein EAF3

State in the Current Structure

Other States of the Same Protein in the Database

RCO1 isoform 1

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

来源 Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)