SAXSdb — 2jmi

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

Protein YNG1

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 141–219	Fragment：PHD finger	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions：pH 7.5；20 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition：0.54 mM [U-13C, U-15N] YNG1_PHD, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.6 mM [U-15N] YNG1_PHD, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition：0.54 mM [U-13C, U-15N] YNG1_PHD, 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 2JMI	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JMJ NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide Deposited 2006-11-15	Different oligomeric state Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 141–219（79 aa） Fragment：PHD finger	Not recorded	ZN ZINC ION × 2	SOLUTION NMR NMR measurement conditions pH 7.5；20 K；Ionic strength (raw mmCIF value) 50；Pressure ambient NMR sample composition 0.52 mM [U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O \| 90% H2O/10% D2O NMR sample composition 0.48 mM [U-13C; U-15N] YNG1_PHD, 2.5 mM H3(1-9)K4me3, 2 mM DTT, 50 mM potassium chloride, 20 mM sodium phosphate, 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different oligomeric state 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 113–124（12 aa） Fragment：UNP residues 113-124	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 113–124（12 aa） Fragment：UNP residues 113-124	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 113–124（12 aa） Fragment：UNP residues 113-124	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 113–124（12 aa） Fragment：UNP residues 113-124	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；40% PEG 400, 0.1 M Tris pH 8.5, 0.2 M LiSO4	Resolution 1.93 Å R-free 0.221
9UUO The NuA3 histone acetyltransferase complex Deposited 2025-05-07	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 C 1–219（219 aa）	Not recorded	ZN ZINC ION × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.68 Å
9UUS The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail Deposited 2025-05-08	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain C 1–219（219 aa）	Not recorded	ZN ZINC ION × 5 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.20 Å
9VKW Cryo-EM structure of the NuA3 complex bound to Ace-coenzyme A Deposited 2025-06-24	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 C 1–219（219 aa）	Not recorded	ZN ZINC ION × 4 ACO ACETYL COENZYME *A × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.13 Å

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	YNG1_YEAST
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 12–90； UniProt 141–219

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	2jmi
Deposition date deposition_date	2006-11-15
Structure title title	NMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state
Keywords keywords	PHD, Histone, Recognition, Yeast, PROTEIN BINDING; PROTEIN BINDING
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	11.55 Å
Radius of gyration Rg (electron density) rg_electron	11.74 Å
Forward intensity I(0) i0	316191000.00
Molecular weight molecular_weight	140350.0 kDa
Excluded volume excluded_volume	170750 Å³
Envelope volume envelope_volume	19868 Å³
Hydration-shell volume shell_volume	11530 Å³
Envelope diameter envelope_diameter	51.8 Å
Shell Rg shell_rg	20.46 Å
Envelope Rg envelope_rg	16.09 Å
Shape Rg shape_rg	11.78 Å
Total Rg total_rg	11.83 Å
Total atoms total_atoms	18520
Residues n_residues	1200
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	50.6 Å
Rg (real space) rg_real	11.68 Å
Rg uncertainty (real space) rg_real_error	0.70 Å
I(0) (real space) i0_real	3.1620e+08
I(0) uncertainty (real space) i0_real_error	4.2490e+06
Rg (reciprocal space) rg_reciprocal	11.68 Å
I(0) (reciprocal space) i0_reciprocal	316200000.0000
Solution quality estimate total_estimate	0.7013
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	12.8 Å
Skewness Skewness skewness	0.613
Kurtosis Kurtosis kurtosis	0.276
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	42510.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.315; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.167; Smooth: 0.999

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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	d2jmia_
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	2jmiA00
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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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
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	—

Description description	Protein YNG1
Molecular weight formula_weight	10269.6 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	18520

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

NMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state

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

Protein YNG1

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

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)

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/jm/2jmi/2jmi.fit
pddf	/app/data/pr_computation/jm/2jmi/2jmi.pr.out
profile	/app/data/saxs_computation/jm/2jmi/2jmi.dat