7yta

crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide

Method: X-RAY DIFFRACTION D_max: 99.0 Å Quality: GOOD

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

AGDP3 AGD1-2

Nicotiana tabacum

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 1–150	Mutation：L12I,T13A,A16S,V17I,L110M,E137Q	H3(1-15)K9me2 peptide × 1 （P59226）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 1–150	Mutation：L12I,T13A,A16S,V17I,L110M,E137Q	H3(1-15)K9me2 peptide × 1 （P59226）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–150	Mutation：L12I,T13A,A16S,V17I,L110M,E137Q	H3(1-15)K9me2 peptide × 1 （P59226）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	A0A1S4CD95_TOBAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–151； UniProt 1–150 Author chain B； PDBConstruct 2–151； UniProt 1–150 Author chain C； PDBConstruct 2–151； UniProt 1–150

H3(1-15)K9me2 peptide

OrganismNot specified

UniProt P59226

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 2–16	Non-standard monomer：Yes (specific site not provided by mmCIF)	AGDP3 AGD1-2 × 1 （A0A1S4CD95）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Q； UniProt 2–16	Non-standard monomer：Yes (specific site not provided by mmCIF)	AGDP3 AGD1-2 × 1 （A0A1S4CD95）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271
3	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain R； UniProt 2–16	Non-standard monomer：Yes (specific site not provided by mmCIF)	AGDP3 AGD1-2 × 1 （A0A1S4CD95）	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；293 K；25% PEG 1500, 0.1 M sodium chloride and 0.1 M bis-Tris propane, pH 9.0	Resolution 2.31 Å R-free 0.271

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 7YTA	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4IUR crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：H3(1-15) K9me3 peptide (unp residues 2-16)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.50 Å R-free 0.256
4IUT crystal structure of SHH1 SAWADEE domain in complex with H3K9me2 peptide Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：H3(1-15) K9me2 peptide (unp residues 2-16)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.248
4IUU Crystal structure of SHH1 SAWADEE domain in complex with H3K9me1 peptide Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：H3(1-15) K9me1 peptide (unp residues 2-16)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.269
4IUV crystal structure of SHH1 SAWADEE domain in complex with H3K4me1K9me1 peptide Deposited 2013-01-21	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 2–16（15 aa） Fragment：H3(1-15)K4me1K9me1 peptide (unp residues 2-16)	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 1 CVM CYMAL-4 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.2 M NH4F, 20% PEG 3350, 7.6 mM 4-Cyclohexyl-1-Butyl-D-Maltoside , VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.80 Å R-free 0.253
5VAH Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26 Deposited 2017-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 22–36（15 aa） Fragment：residues 22-36	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)	Resolution 2.40 Å R-free 0.281
5VAH Crystal structure of ATXR5 SET domain in complex with histone H3 di-methylated on R26 Deposited 2017-03-26	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 22–36（15 aa） Fragment：residues 22-36	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；50% polypropylene glycol 400, 5% DMSO, 0.1 M HEPES-NaOH (pH 6.0)	Resolution 2.40 Å R-free 0.281
5VBC Crystal structure of ATXR5 in complex with histone H3.1 Deposited 2017-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 24–37（14 aa） Fragment：residues 24-37	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 DMS DIMETHYL SULFOXIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；50% polypropylene glycol 400, 100mM Na-Hepes pH 6.0 and 5% DMSO	Resolution 2.10 Å R-free 0.234
5VBC Crystal structure of ATXR5 in complex with histone H3.1 Deposited 2017-03-29	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 24–37（14 aa） Fragment：residues 24-37	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；50% polypropylene glycol 400, 100mM Na-Hepes pH 6.0 and 5% DMSO	Resolution 2.10 Å R-free 0.234
5YKO Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide Deposited 2017-10-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.2M Na2SO4, 20% PEG 3350, 0.1M bis-tris propane, pH 6.5	Resolution 2.90 Å R-free 0.244
5Z8L crystal structure of Arabidopsis thaliana EBS in complex with an H3K27me3 peptide Deposited 2018-01-31	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 21–36（16 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.2M sodium acetate, 20% PEG 3350	Resolution 2.00 Å R-free 0.230
5Z8N Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide Deposited 2018-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES, pH 6.5, 40% PEG 200	Resolution 3.10 Å R-free 0.252
5Z8N Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide Deposited 2018-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES, pH 6.5, 40% PEG 200	Resolution 3.10 Å R-free 0.252
5Z8N Crystal structure of Arabidopsis thaliana EBS C-terminal deletion construct in complex with an H3K4me2 peptide Deposited 2018-01-31	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain R 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1M MES, pH 6.5, 40% PEG 200	Resolution 3.10 Å R-free 0.252
5ZNP Crystal structure of PtSHL in complex with an H3K4me3 peptide Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium acetate, 20% PEG 3350	Resolution 2.80 Å R-free 0.293
5ZNP Crystal structure of PtSHL in complex with an H3K4me3 peptide Deposited 2018-04-10	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；0.2 M potassium acetate, 20% PEG 3350	Resolution 2.80 Å R-free 0.293
5ZNR Crystal structure of PtSHL in complex with an H3K27me3 peptide Deposited 2018-04-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 21–37（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；277 K；0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M CAPS, pH 10.5	Resolution 3.20 Å R-free 0.232
5ZNR Crystal structure of PtSHL in complex with an H3K27me3 peptide Deposited 2018-04-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 21–37（17 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；277 K；0.2 M lithium sulfate, 2.0 M ammonium sulfate, 0.1 M CAPS, pH 10.5	Resolution 3.20 Å R-free 0.232
5ZWX Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide Deposited 2018-05-17	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–16（15 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 6.5；277 K；15% PEG 20000, 0.1M MES, pH 6.5	Resolution 1.90 Å R-free 0.211
5ZWX Crystal structure of Raphanus sativus AGDP1 AGD12 in complex with an H3K9me2 peptide Deposited 2018-05-17	Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Q 2–16（15 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 6.5；277 K；15% PEG 20000, 0.1M MES, pH 6.5	Resolution 1.90 Å R-free 0.211
6IP4 Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide Deposited 2018-11-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 25–36（12 aa） Fragment：UNP residues 25-36	Non-standard monomer：Yes (specific site not provided by mmCIF)	NI NICKEL (II) ION × 1 ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 SO4 SULFATE ION × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；277 K；0.1M MES, pH 6.5, 8% dioxane, and 1.6M ammonium sulfate	Resolution 2.60 Å R-free 0.246
6LQE Crystal structure of Arabidopsis ARID5 PHD finger in complex with H3K4me3 peptide Deposited 2020-01-13	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；0.1 M sodium acetate, pH 4.6, 30% PEG 300	Resolution 1.90 Å R-free 0.241
6LQF Crystal structure of Arabidopsis ARID5 ARID-PHD cassette in complex with H3K4me3 peptide and DNA Deposited 2020-01-13	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric	Chain P 2–16（15 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 5；298 K；0.1 M sodium acetate, pH 5.0, 15% MPD	Resolution 1.50 Å R-free 0.192
7CCE crystal structure of Arabidopsis AIPP3 BAH domain in complex with an H3K27me3 peptide Deposited 2020-06-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 21–38（18 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；277 K；0.1 M HEPES, pH 7.0, and 2.4 M ammonium sulfate	Resolution 2.40 Å R-free 0.266
7DE9 crystal structure of Arabidopsis RDM15 tudor domain in complex with an H3K4me1 peptide Deposited 2020-11-03	Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–16（15 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 8.5；293 K；0.1 M Tris-HCl, pH 8.5, and 20% PEG 1000	Resolution 1.71 Å R-free 0.202
7T7T Structure of TSK/BRU1 bound to histone H3.1 Deposited 2021-12-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain W 2–46（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294.15 K；25% 1,2-Propanediol, 20% glycerol, 0.1M sodium potassium phosphate pH 6	Resolution 3.17 Å R-free 0.318
7T7T Structure of TSK/BRU1 bound to histone H3.1 Deposited 2021-12-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain X 2–46（45 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6；294.15 K；25% 1,2-Propanediol, 20% glycerol, 0.1M sodium potassium phosphate pH 6	Resolution 3.17 Å R-free 0.318
8J90 Cryo-EM structure of DDM1-nucleosome complex Deposited 2023-05-02	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: 11-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 ETHANE	Resolution 4.71 Å
8J91 Cryo-EM structure of nucleosome containing Arabidopsis thaliana histones Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state 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 ETHANE	Resolution 2.90 Å
8J92 Cryo-EM structure of nucleosome containing Arabidopsis thaliana H2A.W Deposited 2023-05-02	Different construct Different mutation/modification Different oligomeric state 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 ETHANE	Resolution 2.90 Å
8JG4 Crystal Structure of YAF9A YEATS bound to H3K27cr peptide Deposited 2023-05-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 25–32（8 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；291 K；0.1 M Tris pH 8.5, 0.2 M Li2SO4, 25% PEG 3350	Resolution 2.30 Å R-free 0.212
8JG4 Crystal Structure of YAF9A YEATS bound to H3K27cr peptide Deposited 2023-05-19	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 25–32（8 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；291 K；0.1 M Tris pH 8.5, 0.2 M Li2SO4, 25% PEG 3350	Resolution 2.30 Å R-free 0.212
8KCB Complex of DDM1-nucleosome(H2A) complex with DDM1 bound to SHL2 Deposited 2023-08-07	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 E 1–136（136 aa） Chain F 1–136（136 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
8KCC Complex of DDM1-nucleosome(H2A.W) complex with DDM1 bound to SHL2 Deposited 2023-08-07	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 E 1–136（136 aa） Chain F 1–136（136 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 3.10 Å
8WH5 Structure of DDM1-nucleosome complex in the apo state Deposited 2023-09-22	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	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.58 Å
8WH8 Structure of DDM1-nucleosome complex in ADP state Deposited 2023-09-22	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 × 9 PDB declaration: undecameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.60 Å
8WH9 Structure of DDM1-nucleosome complex in ADP-BeFx state Deposited 2023-09-22	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 × 9 PDB declaration: undecameric	Chain A 1–136（136 aa） Chain E 1–136（136 aa）	Not recorded	BEF BERYLLIUM TRIFLUORIDE ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.31 Å
8WHA Structure of DDM1-nucleosome complex in the ADP-BeFx state with DDM1 bound to SHL2 and SHL-2 Deposited 2023-09-22	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	BEF BERYLLIUM TRIFLUORIDE ION × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.05 Å
8WHB Structure of nucleosome core particle of Arabidopsis thaliana Deposited 2023-09-23	Different construct Different mutation/modification Different oligomeric state 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 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.17 Å
9K3Z Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.75 Å
9K40 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.15 Å
9K41 Cryo-EM structure of Arabidopsis thaliana H2A.W-nucleosome with Arabidopsis native 147bp DNA 15.2.2 (C2 symmetry) Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.81 Å
9K42 Cryo-EM structure of Arabidopsis thaliana H2A-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å
9K43 Cryo-EM structure of Arabidopsis thaliana H2A.Z-nucleosome with 147bp Widom 601 DNA (C2 symmetry) Deposited 2024-10-21	Different construct Different mutation/modification Different oligomeric state 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 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.87 Å
9M4R crystal structure of Arabidopsis thaliana ING1 PHD finger in complex with an H3K4me3 peptide Deposited 2025-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6；293 K；40% PEG400, 5% PEG3000, and 0.1M MES, pH 6.0	Resolution 1.70 Å R-free 0.200
9M4S crystal structure of Arabidopsis thaliana ING2 PHD finger in complex with an H3K4me3 peptide Deposited 2025-03-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain P 2–11（10 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ZN ZINC ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；293 K；0.1M NiCl2, 20% PEG2000 MME, and 0.1M Tris, pH 8.5	Resolution 1.60 Å R-free 0.225

36 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	H32_ARATH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain P； PDBConstruct 1–15； UniProt 2–16 Author chain Q； PDBConstruct 1–15； UniProt 2–16 Author chain R； PDBConstruct 1–15； UniProt 2–16

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	7yta
Deposition date deposition_date	2022-08-13
Structure title title	crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide
Keywords keywords	AGENET domain, ROS1, H3K9me2 binding, GENE REGULATION; GENE REGULATION
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	28.29 Å
Radius of gyration Rg (electron density) rg_electron	27.94 Å
Forward intensity I(0) i0	40860100.00
Molecular weight molecular_weight	50847.0 kDa
Excluded volume excluded_volume	64134 Å³
Envelope volume envelope_volume	84234 Å³
Hydration-shell volume shell_volume	26917 Å³
Envelope diameter envelope_diameter	105.8 Å
Shell Rg shell_rg	33.08 Å
Envelope Rg envelope_rg	28.08 Å
Shape Rg shape_rg	27.89 Å
Total Rg total_rg	28.66 Å
Total atoms total_atoms	3607
Residues n_residues	440
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	99.0 Å
Rg (real space) rg_real	28.48 Å
Rg uncertainty (real space) rg_real_error	0.80 Å
I(0) (real space) i0_real	4.0860e+07
I(0) uncertainty (real space) i0_real_error	6.2370e+05
Rg (reciprocal space) rg_reciprocal	28.43 Å
I(0) (reciprocal space) i0_reciprocal	40860000.0000
Solution quality estimate total_estimate	0.8575
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.3 Å
Skewness Skewness skewness	0.480
Kurtosis Kurtosis kurtosis	-0.284
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	7181000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.815; Smooth: 0.977

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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	AGDP3 AGD1-2
Molecular weight formula_weight	17335.5 kDa
Mutation mutation	L12I,T13A,A16S,V17I,L110M,E137Q
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	3677

SMRGGRHQKYSHIAKGSIVEVTSDEEGFKGVWFEATVLGASSPGSKSKEVWVEYKSIVAEENGSEPLKEVLHVSFIRPVPPVEKIERFELYDVVDAFHKDGWWTGVVTRVMEDSRYQVTFDNPPDELEFGVSELRFHQKWVKGKWVRPGKQ

来源 Source

来源生物 organism	Nicotiana tabacum
通用名 common_name	common tobacco
NCBI Class编号 ncbi_taxonomy_id	4097
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	H3(1-15)K9me2 peptide
Molecular weight formula_weight	1592.8 kDa
Source method src_method	syn
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	P,Q,R

ARTKQTARKSTGGKA

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	70

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8. Citations (1)

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Unit-cell length a length_a	70.741 Å
Unit-cell length b length_b	70.741 Å
Unit-cell length c length_c	217.989 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	24

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.310 Å
Low-resolution limit resolution_low	27.470 Å
R factor r_factor	0.2487
R_work r_work	0.2474
R_free r_free	0.2708

fit	/app/data/saxs_computation/yt/7yta/7yta.fit
pddf	/app/data/pr_computation/yt/7yta/7yta.pr.out
profile	/app/data/saxs_computation/yt/7yta/7yta.dat

crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide

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

AGDP3 AGD1-2

State in the Current Structure

Other States of the Same Protein in the Database

H3(1-15)K9me2 peptide

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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)