Current Protein Identity：P59226
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Difference tags compare only the current result set; every original PDB and assembly record remains separate.
Related-Structure Differences
Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.
| PDB Entry | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Experimental Method | Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 4IUR crystal structure of SHH1 SAWADEE domain in complex with H3K9me3 peptide Deposited 2013-01-21 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 2 PDB declaration: tetrameric（4） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 |
| 7YTA crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide Deposited 2022-08-13 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 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 |
| 7YTA crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide Deposited 2022-08-13 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 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 |
| 7YTA crystal structure of NtAGDP3 AGD1-2 in complex with an H3K9me2 peptide Deposited 2022-08-13 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain R
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 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 |
| 8J90 Cryo-EM structure of DDM1-nucleosome complex Deposited 2023-05-02 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
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 |