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NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide

Method: SOLUTION NMR D_max: 49.4 Å Quality: REASONABLE

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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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 141–219	Fragment：PHD finger	Histone H3 × 1 （P61830） 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

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 2JMJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JMI NMR solution structure of PHD finger fragment of Yeast Yng1 protein in free state Deposited 2006-11-15	Different oligomeric state Different experimental conditions	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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 0.54 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
8U77 Crystal structure of Taf14 in complex with Yng1 Deposited 2023-09-14	Different construct 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 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 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 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

Histone H3

OrganismNot specified

UniProt P61830

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain P； UniProt 2–10	Non-standard monomer：Yes (specific site not provided by mmCIF)	Protein YNG1 × 1 （Q08465） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 2JMJ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1ID3 CRYSTAL STRUCTURE OF THE YEAST NUCLEOSOME CORE PARTICLE REVEALS FUNDAMENTAL DIFFERENCES IN INTER-NUCLEOSOME INTERACTIONS Deposited 2001-04-03	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 × 8 PDB declaration: decameric	Chain A 1–135（135 aa） Chain E 1–135（135 aa）	Not recorded	MN MANGANESE (II) ION × 17	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；292 K；Manganese chloride, Potassium chloride, cacodylate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 292K	Resolution 3.10 Å R-free 0.292
1QSN CRYSTAL STRUCTURE OF TETRAHYMENA GCN5 WITH BOUND COENZYME A AND HISTONE H3 PEPTIDE Deposited 1999-06-22	Different construct Different mutation/modification 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 10–20（11 aa） Fragment：11 MER PEPTIDE (RESIDUES 9 - 19)	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；TRIS, AMMONIUM SULFATE, MANGANESE CHLORIDE, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 298.00K	Resolution 2.20 Å R-free 0.266
2H2G The Structural Basis of Sirtuin substrate affinity Deposited 2006-05-18	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 113–123（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293.15 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293.15K	Resolution 1.63 Å R-free 0.226
2H2G The Structural Basis of Sirtuin substrate affinity Deposited 2006-05-18	Different construct Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 113–123（11 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；293.15 K；20% PEG, pH 9.6, VAPOR DIFFUSION, HANGING DROP, pH 7.5, temperature 293.15K	Resolution 1.63 Å R-free 0.226
2IDC Structure of the Histone H3-Asf1 Chaperone Interaction Deposited 2006-09-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 122–135（14 aa） Fragment：Asf1, residues 2-155 and H3, residues 121-134	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；292 K；Tris-HCl, Li2SO4, PEG 4000, glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.20 Å R-free 0.239
2RNW The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the Human Transcriptional Co-Activators PCAf and CBP Deposited 2008-02-03	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 2–16（15 aa） Fragment：UNP residues 2-16	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
2RNX The Structural Basis for Site-Specific Lysine-Acetylated Histone Recognition by the Bromodomains of the HUman Transcriptional Co-Activators PCAF and CBP Deposited 2008-02-03	Different construct Different ligand/ion Different experimental conditions	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 32–43（12 aa） Fragment：UNP residues 32-43	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.5 mM [U-100% 13C; U-100% 15N] potassium phosphate, 100% D2O \| 100% D2O	Resolution not provided
3Q33 Structure of the Rtt109-AcCoA/Vps75 Complex and Implications for Chaperone-Mediated Histone Acetylation Deposited 2010-12-21	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 D 1–14（14 aa） Fragment：unp residues 1-14	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACO ACETYL COENZYME A × 2 EDO* 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；298 K；10.0% (v/v) PEG 8000 8% (v/v) ethylene glycol 100 mM Hepes, VAPOR DIFFUSION, HANGING DROP, temperature 298K, pH 7.5	Resolution 2.80 Å R-free 0.255
4JJN Crystal structure of heterochromatin protein Sir3 in complex with a silenced yeast nucleosome Deposited 2013-03-08	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 × 10 PDB declaration: dodecameric	Chain A 2–136（135 aa） Chain E 2–136（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.05 M sodium cacodylate, 32% 2-methyl-2,4-pentanediol (MPD), pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 3.09 Å R-free 0.255
4KUD Crystal structure of N-terminal acetylated Sir3 BAH domain D205N mutant in complex with yeast nucleosome core particle Deposited 2013-05-22	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 A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；289 K；16% PEG 400, 0.1M KCl, 0.01M CaCl2, 0.05M sodium citrate(pH4.8), VAPOR DIFFUSION, HANGING DROP, temperature 289K	Resolution 3.20 Å R-free 0.237
4PSX Crystal structure of histone acetyltransferase complex Deposited 2014-03-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain Y 2–16（15 aa） Fragment：UNP residues 2-16	Not recorded	COA COENZYME A × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M potassium sodium tartrate, 20%(w/v) polyethylene glycol 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.51 Å R-free 0.223
4PSX Crystal structure of histone acetyltransferase complex Deposited 2014-03-08	Different construct Different mutation/modification 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 P 2–16（15 aa） Fragment：UNP residues 2-16	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；0.2M potassium sodium tartrate, 20%(w/v) polyethylene glycol 3,350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K	Resolution 2.51 Å R-free 0.223
5ZBA Crystal structure of Rtt109-Asf1-H3-H4-CoA complex Deposited 2018-02-10	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 × 4 PDB declaration: tetrameric	Chain C 1–136（136 aa）	Not recorded	COA COENZYME A × 1 IOD IODIDE ION × 37	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide	Resolution 3.50 Å R-free 0.294
5ZBB Crystal structure of Rtt109-Asf1-H3-H4 complex Deposited 2018-02-10	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 × 4 PDB declaration: tetrameric	Chain C 1–136（136 aa）	Not recorded	IOD IODIDE ION × 23 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5；277 K；100mM sodium citrate, pH 5.0, 22% PEG 1500, 400mM sodium iodide	Resolution 3.60 Å R-free 0.264
6GEJ Chromatin remodeller-nucleosome complex at 3.6 A resolution. Deposited 2018-04-26	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 × 18 PDB declaration: eicosameric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6GEN Chromatin remodeller-nucleosome complex at 4.5 A resolution. Deposited 2018-04-27	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 × 18 PDB declaration: eicosameric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
6J2P Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 Deposited 2019-01-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 2–8（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5	Resolution 2.85 Å R-free 0.288
6J2P Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 Deposited 2019-01-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 2–8（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5	Resolution 2.85 Å R-free 0.288
6J2P Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 Deposited 2019-01-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain H 2–8（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5	Resolution 2.85 Å R-free 0.288
6J2P Crystal structure of Saccharomyces cerevisiae Spp1 in complex with H3K4me3 Deposited 2019-01-02	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 2–8（7 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M ammonium sulfate, 20% PEG3350, 0.1 M HEPES ph 7.5	Resolution 2.85 Å R-free 0.288
6KMJ Crystal structure of Sth1 bromodomain in complex with H3K14Ac Deposited 2019-07-31	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 7–22（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；1% w/v tryptone, 1 mM sodium azide, 50 mM HEPES sodium pH 7.0, 20% w/v PEG 3350	Resolution 1.40 Å R-free 0.188
7E9C Cryo-EM structure of the 1:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04	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 × 9 PDB declaration: undecameric	Chain A 1–134（134 aa） Chain E 1–134（134 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7E9F Cryo-EM structure of the 2:1 Orc1 BAH domain in complex with nucleosome Deposited 2021-03-04	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: dodecameric	Chain A 1–134（134 aa） Chain E 1–134（134 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.00 Å
7F4A Crystal structure of Taf14 YEATS domain in complex with H3K9bz peptide Deposited 2021-06-18	Different construct 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 6–14（9 aa）	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, SITTING DROP；pH 6；289 K；48% PEG 600, 0.04M citric acid	Resolution 2.00 Å R-free 0.204
7F4E Crystal structure of Hst2 in complex with H3K9bz peptide Deposited 2021-06-18	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 6–15（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；25% (w/v) PEG 1500, 0.1M MMT/Sodium hydroxide	Resolution 1.78 Å R-free 0.216
7K7G nucleosome and Gal4 complex Deposited 2020-09-22	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 A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.3 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7UQJ Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II Deposited 2022-04-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain G 1–25（25 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 AGS PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER × 5 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6；Solution was made fresh and detergent was added to solve preference orientation issue. cryo-EM vitrification conditions Cryogen ETHANE；Blot 3S, blot forth 3	Resolution 3.00 Å
7XAY Crystal structure of Hat1-Hat2-Asf1-H3-H4 Deposited 2022-03-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 5 PDB declaration: pentameric	Chain D 2–136（135 aa）	Not recorded	COA COENZYME A × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；100 mM Bis-Tris propane, pH 6.5, 20% PEG-3350, and 200 mM sodium nitrate	Resolution 3.30 Å R-free 0.256
7Z0O Structure of transcription factor UAF in complex with TBP and 35S rRNA promoter DNA Deposited 2022-02-23	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 × 8 PDB declaration: decameric	Chain A 1–136（136 aa） Chain C 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.80 Å
8GHN Composite model of the yeast Hir Complex with Asf1/H3/H4 Deposited 2023-03-10	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 × 15 PDB declaration: 15-meric	Chain M 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.6 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.96 Å
8QKU SWR1-nucleosome complex in configuration 1 Deposited 2023-09-18	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 × 18 PDB declaration: eicosameric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
8QKV SWR1-nucleosome complex in configuration 2 Deposited 2023-09-18	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 × 18 PDB declaration: eicosameric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.70 Å
8QYV SWR1-hexasome complex Deposited 2023-10-26	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 × 17 PDB declaration: 19-meric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Mutation：Q120M, K121P, K125Q Mutation：Q120M, K121P, K125Q	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
8QZ0 SWR1-hexasome-dimer complex Deposited 2023-10-26	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 × 20 PDB declaration: 22-meric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Mutation：Q120M, K121P, K125Q Mutation：Q120M, K121P, K125Q	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.80 Å
9C9G S.c INO80 in complex with S.c 0/80 nucleosome Deposited 2024-06-13	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 × 18 PDB declaration: 20-meric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 2.91 Å
9C9S S.c INO80 in complex with S.c 0/40 nucleosome, Class 1 Deposited 2024-06-15	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 × 18 PDB declaration: 20-meric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.09 Å
9C9T S.c INO80 in complex with S.c 0/40 nucleosome, Class 2 Deposited 2024-06-15	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 × 18 PDB declaration: 20-meric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.16 Å
9CAU DeltaArp8 INO80 bound to S.c 0/40 nucleosome, Nucleosome Deposited 2024-06-17	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 × 8 PDB declaration: decameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 4.18 Å
9CB7 DeltaNhp10 INO80 bound to S.c 0/40 nucleosome, Ino80-Nucleosome Deposited 2024-06-18	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 A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 4.04 Å
9FBW SWR1 lacking Swc5 subunit in complex with hexasome Deposited 2024-05-14	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 × 16 PDB declaration: 18-meric	Chain A 1–136（136 aa） Chain B 1–136（136 aa）	Mutation：Q120M, K121P, K125Q Mutation：Q120M, K121P, K125Q	ADP ADENOSINE-5'-DIPHOSPHATE × 8 BEF BERYLLIUM TRIFLUORIDE ION × 2 MG MAGNESIUM ION × 8 ZN ZINC ION × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.40 Å
9OB1 S.c INO80 in complex with Yeast 0/80 nucleosome, Apo State Deposited 2025-04-21	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 × 18 PDB declaration: eicosameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 6	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen OTHER	Resolution 3.20 Å
9UUS The NuA3 histone acetyltransferase complex bound to acetyl-CoA and H3 tail Deposited 2025-05-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain H 2–22（21 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

37 other PDB entries and 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H3_YEAST
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–9； UniProt 2–10

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

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2jmj
Deposition date deposition_date	2006-11-15
Structure title title	NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide
Keywords keywords	Histone, PHD, H3K4me3, complex, 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	11.91 Å
Radius of gyration Rg (electron density) rg_electron	12.09 Å
Forward intensity I(0) i0	414355000.00
Molecular weight molecular_weight	162140.0 kDa
Excluded volume excluded_volume	198430 Å³
Envelope volume envelope_volume	22292 Å³
Hydration-shell volume shell_volume	12375 Å³
Envelope diameter envelope_diameter	54.3 Å
Shell Rg shell_rg	21.14 Å
Envelope Rg envelope_rg	16.66 Å
Shape Rg shape_rg	12.11 Å
Total Rg total_rg	12.23 Å
Total atoms total_atoms	21880
Residues n_residues	1360
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	49.4 Å
Rg (real space) rg_real	12.01 Å
Rg uncertainty (real space) rg_real_error	0.46 Å
I(0) (real space) i0_real	4.1440e+08
I(0) uncertainty (real space) i0_real_error	4.5190e+06
Rg (reciprocal space) rg_reciprocal	12.00 Å
I(0) (reciprocal space) i0_reciprocal	414400000.0000
Solution quality estimate total_estimate	0.7369
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	13.8 Å
Skewness Skewness skewness	0.605
Kurtosis Kurtosis kurtosis	0.329
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	75060.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.401; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.375; Smooth: 0.998

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Protein YNG1
Molecular weight formula_weight	10269.6 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	21880

GPLGSHMASEFINQGDVTEGNNNQEEVYCFCRNVSYGPMVACDNPACPFEWFHYGCVGLKQAPKGKWYCSKDCKEIANQRSKSKRQKRRK

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	Histone H3
Molecular weight formula_weight	1105.3 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P

ARTKQTARK

Entity 3 Entity 3 non-polymer

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

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	2jmjA00
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	—

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

NMR solution structure of the PHD domain from the yeast YNG1 protein in complex with H3(1-9)K4me3 peptide

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

Histone H3

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)