SAXSdb — 2mum

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

Chromatin modification-related protein YNG2

Saccharomyces cerevisiae 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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 222–271	Fragment：PHD-type domain residues 222-271	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 6.5；298 K；Ionic strength (raw mmCIF value) 300；Pressure ambient NMR sample composition：0.5 mM [U-13C; U-15N] protein, 300 mM sodium chloride, 2.7 mM potassium chloride, 2 mM potassium phosphate, 10 mM sodium phosphate, 0.05 mM CHAPS, 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 2MUM	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5J9Q Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain H 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 3.25 Å R-free 0.273
5J9Q Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 3.25 Å R-free 0.273
5J9Q Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain K 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 3.25 Å R-free 0.273
5J9T Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM HEPES (pH 7.5), 6% 1,6-Hexanediol, 7% PEG 8000, 5% ethylene glycol, 10mM DTT.	Resolution 2.70 Å R-free 0.219
5J9T Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM HEPES (pH 7.5), 6% 1,6-Hexanediol, 7% PEG 8000, 5% ethylene glycol, 10mM DTT.	Resolution 2.70 Å R-free 0.219
5J9T Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100mM HEPES (pH 7.5), 6% 1,6-Hexanediol, 7% PEG 8000, 5% ethylene glycol, 10mM DTT.	Resolution 2.70 Å R-free 0.219
5J9U Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；298 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 2.95 Å R-free 0.246
5J9U Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；298 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 2.95 Å R-free 0.246
5J9U Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain K 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；298 K；100mM NaCitrate (pH 6.5), 1.79M ammonium sulfate, 5%(w/v) glycerol	Resolution 2.95 Å R-free 0.246
5J9W Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain H 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100 mM HEPES (pH 7.5), 9% PEG 20000, 8% glycerol, 7% 2-Propanol, 10% 1,6-Hexanediol, 10 mM DTT	Resolution 2.80 Å R-free 0.271
5J9W Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain D 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100 mM HEPES (pH 7.5), 9% PEG 20000, 8% glycerol, 7% 2-Propanol, 10% 1,6-Hexanediol, 10 mM DTT	Resolution 2.80 Å R-free 0.271
5J9W Crystal structure of the NuA4 core complex Deposited 2016-04-11	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain L 1–120（120 aa） Fragment：UNP residues 1-120	Not recorded	ACO ACETYL COENZYME *A × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；289 K；100 mM HEPES (pH 7.5), 9% PEG 20000, 8% glycerol, 7% 2-Propanol, 10% 1,6-Hexanediol, 10 mM DTT	Resolution 2.80 Å R-free 0.271
7VVU NuA4 HAT module bound to the nucleosome Deposited 2021-11-09	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 V 1–282（282 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 3.40 Å
7VVZ NuA4 bound to the nucleosome Deposited 2021-11-09	Different construct 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 V 1–282（282 aa）	Not recorded	CMC CARBOXYMETHYL COENZYME A × 1 MG MAGNESIUM ION × 2 ATP* ADENOSINE-5'-TRIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen NITROGEN	Resolution 8.80 Å

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

View Construct and Data Evidence

UniProt name	YNG2_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–50； UniProt 222–271

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	2mum
Deposition date deposition_date	2014-09-12
Structure title title	Solution structure of the PHD domain of Yeast YNG2
Keywords keywords	PHD finger, Transcription Regulator; Transcription Regulator
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	10.15 Å
Radius of gyration Rg (electron density) rg_electron	10.56 Å
Forward intensity I(0) i0	226796000.00
Molecular weight molecular_weight	121230.0 kDa
Excluded volume excluded_volume	148070 Å³
Envelope volume envelope_volume	13640 Å³
Hydration-shell volume shell_volume	9671 Å³
Envelope diameter envelope_diameter	39.3 Å
Shell Rg shell_rg	17.65 Å
Envelope Rg envelope_rg	12.50 Å
Shape Rg shape_rg	10.59 Å
Total Rg total_rg	10.65 Å
Total atoms total_atoms	15760
Residues n_residues	1000
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	34.0 Å
Rg (real space) rg_real	10.10 Å
Rg uncertainty (real space) rg_real_error	0.38 Å
I(0) (real space) i0_real	2.2680e+08
I(0) uncertainty (real space) i0_real_error	2.3920e+06
Rg (reciprocal space) rg_reciprocal	10.10 Å
I(0) (reciprocal space) i0_reciprocal	226800000.0000
Solution quality estimate total_estimate	0.8899
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.9 Å
Skewness Skewness skewness	0.071
Kurtosis Kurtosis kurtosis	-0.523
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	23060.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 0.994; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.975

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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) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d2muma_
Class class	g — Small proteins
Fold Fold fold	g.50 — FYVE/PHD zinc finger
Superfamily Superfamily superfamily	g.50.1 — FYVE/PHD zinc finger
Family Family family	g.50.1.0 — automated matches

CATH v4.4 (1 domains)

Domain ID domain_id	2mumA00
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	40 — Herpes Virus-1
Homologous superfamily homologous superfamily	10 — Zinc/RING finger domain, C3HC4 (zinc finger)

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8. Citations (1)

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Description description	Chromatin modification-related protein YNG2
Molecular weight formula_weight	5938.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	15760

来源生物 organism	Saccharomyces cerevisiae 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

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

fit	/app/data/saxs_computation/mu/2mum/2mum.fit
pddf	/app/data/pr_computation/mu/2mum/2mum.pr.out
profile	/app/data/saxs_computation/mu/2mum/2mum.dat

Solution structure of the PHD domain of Yeast YNG2

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

Chromatin modification-related protein YNG2

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

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)