SAXSdb — 2dy8

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

Chromo domain protein 1

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 279–347	Fragment：chromodomain 2	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 6.8；293 K；Ionic strength (raw mmCIF value) 300mM NaCl；Pressure ambient NMR sample composition：0.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 100% D2O \| 100% D2O NMR sample composition：0.3-0.5mM chromodomain U-15N; 20mM potassium phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 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 2DY8	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2DY7 Solution structure of the first chromodomain of yeast Chd1 Deposited 2006-09-07	Different construct Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 172–252（81 aa） Fragment：chromodomain 1	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.8；298 K；Ionic strength (raw mmCIF value) 300mM NaCl；Pressure ambient NMR sample composition 0.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 30mM d-DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.5mM chromodomain; 20mM potassium phosphate buffer; 30mM d-DTT; 100% D2O \| 100% D2O NMR sample composition 0.3-0.5mM chromodomain U-15N; 20mM potassium phosphate buffer; 30mM d-DTT; 90% H2O, 10% D2O \| 290% H2O, 10% D2O NMR sample composition 0.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 30mM d-DTT; 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.3-0.5mM chromodomain U-13C,15N; 20mM potassium phosphate buffer; 30mM d-DTT; 100% D2O \| 100% D2O	Resolution not provided
2H1E Tandem chromodomains of budding yeast CHD1 Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 174–339（166 aa） Fragment：chromodomain, residues 174-339 Chain B 174–339（166 aa） Fragment：chromodomain, residues 174-339	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；10mM BTP, 12mM NaCl, 5mM TCEP, 0.9M ammonium sulfate, 3.75% isopropanol, 4.5mg/ml yeast CHD1 tandem chromodomains, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.20 Å R-free 0.246
2H1E Tandem chromodomains of budding yeast CHD1 Deposited 2006-05-16	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 174–339（166 aa） Fragment：chromodomain, residues 174-339 Chain B 174–339（166 aa） Fragment：chromodomain, residues 174-339	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；283 K；10mM BTP, 12mM NaCl, 5mM TCEP, 0.9M ammonium sulfate, 3.75% isopropanol, 4.5mg/ml yeast CHD1 tandem chromodomains, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K, pH 8.00	Resolution 2.20 Å R-free 0.246
2XB0 DNA-binding domain from Saccharomyces cerevisiae chromatin- remodelling protein Chd1 Deposited 2010-04-01	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 1009–1274（266 aa） Fragment：DNA BINDING DOMAIN, RESIDUES 1009-1274	Not recorded	GOL GLYCEROL × 2 CL CHLORIDE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；0.1 M TRIS, PH 8.5, 28% PEG 4K, 0.35 M MGCL2	Resolution 2.00 Å R-free 0.248
3MWY Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler Deposited 2010-05-06	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain W 142–939（798 aa） Fragment：double chromodomains and ATPase motor (UNP residues 142-939)	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；18% PEG 3350; 400 mM K+/Na+ tartrate; 5% xylitol; 10 mM MgCl2; 1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.70 Å R-free 0.318
3MWY Crystal structure of the chromodomain-ATPase portion of the yeast Chd1 chromatin remodeler Deposited 2010-05-06	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain W 142–939（798 aa） Fragment：double chromodomains and ATPase motor (UNP residues 142-939)	Not recorded	AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；298 K；18% PEG 3350; 400 mM K+/Na+ tartrate; 5% xylitol; 10 mM MgCl2; 1 mM ATPgammaS, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 3.70 Å R-free 0.318
3TED Crystal structure of the Chd1 DNA-binding domain in complex with a DNA duplex Deposited 2011-08-12	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1006–1274（269 aa） Fragment：SANT/SLIDE DNA-binding domain, UNP residues 1006-1274	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；14-18% PEG 400 0.1 M BisTris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.00 Å R-free 0.249
5J70 The Chd1 DNA-binding domain in complex with 17mer DNA duplex Deposited 2016-04-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain A 1006–1274（269 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；14% PEG 4000, 0.2M ammonium acetate, 0.01M CaCl2, 0.05 M Na cacodylate, pH 5.5	Resolution 2.96 Å R-free 0.252
5J70 The Chd1 DNA-binding domain in complex with 17mer DNA duplex Deposited 2016-04-05	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein–DNA Monomer；Protein × 1 PDB declaration: trimeric	Chain B 1006–1274（269 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5.5；277 K；14% PEG 4000, 0.2M ammonium acetate, 0.01M CaCl2, 0.05 M Na cacodylate, pH 5.5	Resolution 2.96 Å R-free 0.252
5O9G Structure of nucleosome-Chd1 complex Deposited 2017-06-19	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 W 1–1468（1468 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.80 Å
6G0L Structure of two molecules of the chromatin remodelling enzyme Chd1 bound to a nucleosome Deposited 2018-03-19	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 × 10 PDB declaration: dodecameric	Chain M 1–1468（1468 aa） Chain W 1–1468（1468 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2 BEF BERYLLIUM TRIFLUORIDE ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 10.00 Å
7NKX RNA polymerase II-Spt4/5-nucleosome-Chd1 structure Deposited 2021-02-19	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric	Chain W 1–1468（1468 aa）	Not recorded	ZN ZINC ION × 8 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
7TN2 Composite model of a Chd1-nucleosome complex in the nucleotide-free state derived from 2.3A and 2.7A Cryo-EM maps Deposited 2022-01-20	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain W 118–1274（1157 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7；20 mM HEPES, pH 7.0, 60 mM KCl, 1.5 mM DTT, 1 mM MgCl2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.30 Å
9GD1 Structure of Chd1 bound to a hexasome-nucleosome complex with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 15 PDB declaration: 17-meric	Chain W 1–1468（1468 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
9GD2 Structure of Chd1 bound to a dinucleosome with a dyad-to-dyad distance of 103 bp. Deposited 2024-08-04	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 × 19 PDB declaration: 21-meric	Chain S 1–1468（1468 aa） Chain T 1–1468（1468 aa） Chain W 1–1468（1468 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9GD3 Structure of a mononucleosome bound by one copy of Chd1 with the DBD on the exit-side DNA. Deposited 2024-08-04	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 × 10 PDB declaration: 12-meric	Chain T 1–1468（1468 aa） Chain W 1–1468（1468 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 BEF BERYLLIUM TRIFLUORIDE ION × 1 MG MAGNESIUM ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.00 Å
9N6H 2.54 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 1:1 complex Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric	Chain K 122–956（835 aa） Fragment：residues 122-956	Mutation：L886G, L889G, L891G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.54 Å
9N6I 2.61 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 122–956（835 aa） Chain L 122–956（835 aa）	Mutation：L886G, L889G, L891G Mutation：L886G, L889G, L891G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.61 Å
9N6K 2.88 A S.cerevisiae Chd1[L886G/L889G/L891G]-nucleosome 2:1 complex with DNA-binding domain Deposited 2025-02-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric	Chain K 122–1265（1144 aa） Chain L 122–1265（1144 aa）	Mutation：L886G, L889G, L891G Mutation：L886G, L889G, L891G	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.90 Å
9R5S Structural characterisation of chromatin remodelling intermediates supports linker DNA dependent product inhibition as a mechanism for nucleosome spacing. Deposited 2025-05-09	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric	Chain W 2–1468（1467 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5；20mM Hepes, 120mM Nacl cryo-EM vitrification conditions Cryogen ETHANE；Vitrified carried out in climate chamber with 100% humidity	Resolution 3.80 Å

17 other PDB entries and 20 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	CHD1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–69； UniProt 279–347

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	2dy8
Deposition date deposition_date	2006-09-07
Structure title title	Solution structure of the second chromodomain of yeast Chd1
Keywords keywords	Chromatin remodeling, HYDROLASE; HYDROLASE
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	14.16 Å
Radius of gyration Rg (electron density) rg_electron	13.90 Å
Forward intensity I(0) i0	407933000.00
Molecular weight molecular_weight	165420.0 kDa
Excluded volume excluded_volume	204810 Å³
Envelope volume envelope_volume	30674 Å³
Hydration-shell volume shell_volume	14840 Å³
Envelope diameter envelope_diameter	59.4 Å
Shell Rg shell_rg	23.53 Å
Envelope Rg envelope_rg	18.58 Å
Shape Rg shape_rg	13.88 Å
Total Rg total_rg	14.23 Å
Total atoms total_atoms	22920
Residues n_residues	1380
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	58.6 Å
Rg (real space) rg_real	14.23 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	4.0790e+08
I(0) uncertainty (real space) i0_real_error	5.9100e+06
Rg (reciprocal space) rg_reciprocal	14.22 Å
I(0) (reciprocal space) i0_reciprocal	407900000.0000
Solution quality estimate total_estimate	0.5076
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	15.6 Å
Skewness Skewness skewness	0.406
Kurtosis Kurtosis kurtosis	-0.198
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	137000.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.485; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.372; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2dy8a1
Class class	b — All beta proteins
Fold Fold fold	b.34 — SH3-like barrel
Superfamily Superfamily superfamily	b.34.13 — Chromo domain-like
Family Family family	b.34.13.2 — Chromo domain

CATH v4.4 (1 domains)

Domain ID domain_id	2dy8A00
Class class	2 — Mainly Beta
Architecture architecture	40 — Beta Barrel
Topology topology	50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily	40 —

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8. Citations (1)

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Description description	Chromo domain protein 1
Molecular weight formula_weight	8287.1 kDa
EC 编号 ec_number	3.6.1.-
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	22920

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 BL21(DE3)

fit	/app/data/saxs_computation/dy/2dy8/2dy8.fit
pddf	/app/data/pr_computation/dy/2dy8/2dy8.pr.out
profile	/app/data/saxs_computation/dy/2dy8/2dy8.dat

Solution structure of the second chromodomain of yeast Chd1

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

Chromo domain protein 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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)