Current Protein Identity：P84243
New Search
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 |
|---|---|---|---|---|---|---|---|
| 2L43 Structural basis for histone code recognition by BRPF2-PHD1 finger Deposited 2010-10-01 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–13（12 aa）
|
Mutation：C29S, C36S | ZN ZINC ION × 2 | SOLUTION NMR |
NMR measurement conditions
pH 6.7；293 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition
0.8mM [U-100% 13C; U-100% 15N] protein-1, 1.6mM ZINC ION-2, 20mM Bis-Tris-3, 150mM sodium chloride-4, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.8mM [U-100% 13C; U-100% 15N] protein-5, 1.6mM ZINC ION-6, 20mM Bis-Tris-7, 150mM sodium chloride-8, 100% D2O | 100% D2O
|
Resolution not provided |
| 3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain P
2–14（13 aa）
Fragment：residues in UNP 2-14
|
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；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.286 |
| 3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain Q
2–14（13 aa）
Fragment：residues in UNP 2-14
|
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；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.286 |
| 3ASK Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain R
2–14（13 aa）
Fragment：residues in UNP 2-14
|
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, HANGING DROP；pH 6.5；277 K；0.1M Bis-Tris propane, 200mM sodium citrate, 20% PEG3350, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.90 Å R-free 0.286 |
| 3ASL Structure of UHRF1 in complex with histone tail Deposited 2010-12-16 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–12（11 aa）
Fragment：residues in UNP 2-12
|
Not recorded | ZN ZINC ION × 4 EDO 1,2-ETHANEDIOL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；10mM sodium citrate, 42% PEGMME2000, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.41 Å R-free 0.196 |
| 3AV2 The human nucleosome structure containing the histone variant H3.3 Deposited 2011-02-18 | 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 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.80 Å R-free 0.272 |
| 3JVK Crystal structure of bromodomain 1 of mouse Brd4 in complex with histone H3-K(ac)14 Deposited 2009-09-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
13–20（8 aa）
Fragment：UNP residues 13-20
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 10-times excess of histone peptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.259 |
| 3MUK Crystal structure of Brd4 bromodomain 1 with propionylated histone H3-K(prop)23 Deposited 2010-05-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
22–29（8 aa）
Fragment：histone H3 peptide, UNP residues 22-29
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.75 Å R-free 0.219 |
| 3MUL Crystal structure of Brd4 bromodomain 1 with butyrylated histone H3-K(buty)14 Deposited 2010-05-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
13–20（8 aa）
Fragment：histone H3 peptide, UNP residues 13-20
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；3.6M Na formate, 10% glycerol, soaked with 20-times excess of histone octapeptide, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.65 Å R-free 0.226 |
| 3QL9 Monoclinic complex structure of ATRX ADD bound to histone H3K9me3 peptide Deposited 2011-02-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：K9 trimethylated H3 N-terminal fragment, UNP residues 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2 M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 0.93 Å R-free 0.131 |
| 3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：N-terminal tail, UNP residues 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 3 K POTASSIUM ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.179 |
| 3QLA Hexagonal complex structure of ATRX ADD bound to H3K9me3 peptide Deposited 2011-02-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
2–16（15 aa）
Fragment：N-terminal tail, UNP residues 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.1；277 K；14% PEG 4000, 0.1M MES, 0.2M KCL, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.60 Å R-free 0.179 |
| 3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：N-terminal tail, UNP residues 2-16
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.241 |
| 3QLC Complex structure of ATRX ADD domain bound to unmodified H3 1-15 peptide Deposited 2011-02-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
2–16（15 aa）
Fragment：N-terminal tail, UNP residues 2-16
|
Not recorded | ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；24% PEG 3350, 0.1M HEPES-NaOH, 0.2M KCL, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.50 Å R-free 0.241 |
| 3WTP Crystal Structure of the heterotypic nucleosome containing human CENP-A and H3.3 Deposited 2014-04-14 | Assembly 1 Protein–DNA Heteromer；Protein × 8 PDB declaration: decameric（10） Consistent with all polymers |
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 6；293 K；potassium cacodylate, potassium chloride, manganese chloride, pH 6.0, vapor diffusion, hanging drop, temperature 293K
|
Resolution 2.67 Å R-free 0.270 |
| 4GNE Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-7 Deposited 2012-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–8（7 aa）
Fragment：UNP RESIDUES 2-8
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；283 K；0.1M Tris-HCl pH 7.0, 30% (w/v) PEG 3000, 0.2M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 283K
|
Resolution 1.47 Å R-free 0.178 |
| 4GNF Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3 peptide 1-15 Deposited 2012-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：UNP RESIDUES 2-16
|
Not recorded | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；283 K；0.1M Hepes pH 7.5, 70% v/v MPD, VAPOR DIFFUSION, HANGING DROP, temperature 283K
|
Resolution 1.55 Å R-free 0.205 |
| 4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–16（15 aa）
Fragment：UNP RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 GOL GLYCEROL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
|
Resolution 1.73 Å R-free 0.214 |
| 4GNG Crystal Structure of NSD3 tandem PHD5-C5HCH domains complexed with H3K9me3 peptide Deposited 2012-08-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
2–16（15 aa）
Fragment：UNP RESIDUES 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；283 K；0.1M Mes pH 6.5, 20% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 283K
|
Resolution 1.73 Å R-free 0.214 |
| 4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain E
2–27（26 aa）
Fragment：UNP residues 2-27
|
Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.10 Å R-free 0.221 |
| 4GU0 Crystal structure of LSD2 with H3 Deposited 2012-08-29 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
2–27（26 aa）
Fragment：UNP residues 2-27
|
Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 ZN ZINC ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；0.2M (NH4)2 Tartrate, 0.1M HEPES, 10% PEG20000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 3.10 Å R-free 0.221 |
| 4GUR Crystal structure of LSD2-NPAC with H3 in space group P21 Deposited 2012-08-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–22（21 aa）
Fragment：UNP residues 2-22
|
Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；0.02M Citric acid, 0.03M Bis_tris propane, 10% PEG3350, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.51 Å R-free 0.204 |
| 4GUS Crystal structure of LSD2-NPAC with H3 in space group P3221 Deposited 2012-08-29 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
2–22（21 aa）
Fragment：UNP residues 2-22
|
Mutation：K4M | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 IOD IODIDE ION × 6 GOL GLYCEROL × 2 ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；277 K；0.1M Ammonium Iodide, 0.1M MES, 10% PEG3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.23 Å R-free 0.237 |
| 4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
2–18（17 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；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.96 Å R-free 0.288 |
| 4GY5 Crystal structure of the tandem tudor domain and plant homeodomain of UHRF1 with Histone H3K9me3 Deposited 2012-09-05 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
2–18（17 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；pH 6；291 K；20% PEG 3350, 200mM Ammonium Tartrate, 100mM Bis-Tris, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.96 Å R-free 0.288 |
| 4H9N Complex structure 1 of DAXX/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.209 |
| 4H9O Complex structure 2 of DAXX/H3.3(sub5,G90M)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：G90M, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 10 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.05 Å R-free 0.225 |
| 4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 7 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.242 |
| 4H9P Complex structure 3 of DAXX/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 14 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.8 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.242 |
| 4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 9 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.221 |
| 4H9Q Complex structure 4 of DAXX(E225A)/H3.3(sub5)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 18 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；277 K；1.8 M Na/K-phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.221 |
| 4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 6 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.230 |
| 4H9R Complex structure 5 of DAXX(E225A)/H3.3(sub5,G90A)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：G90A, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 12 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.8；277 K；1.6 M Na/K-phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.20 Å R-free 0.230 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain A
2–136（135 aa）
|
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
2–136（135 aa）
|
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4H9S Complex structure 6 of DAXX/H3.3(sub7)/H4 Deposited 2012-09-24 | Assembly 3 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
2–136（135 aa）
Chain B
2–136（135 aa）
|
Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F Mutation：A75C, F84W, S96A, Y99F, G102A, A111T, M120F | PO4 PHOSPHATE ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.2；293 K；0.1 M Na/K-phosphate, 2.5M NaCl, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.60 Å R-free 0.250 |
| 4HGA Structure of the variant histone H3.3-H4 heterodimer in complex with its chaperone DAXX Deposited 2012-10-07 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain B
1–136（136 aa）
|
Not recorded | PC4 TETRACHLOROPLATINATE(II) × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1M HEPES-Na, pH 7.6, 23% (v/v) PEG 3350, 0.25M Ammonium acetate, 1% Tacsimate pH 7.0, 6% ethanol, VAPOR DIFFUSION, SITTING DROP, temperature 298K
|
Resolution 2.80 Å R-free 0.271 |
| 4N4I Crystal structure of the Bromo-PWWP of the mouse zinc finger MYND-type containing 11 isoform alpha in complex with histone H3.3K36me3 Deposited 2013-10-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
20–43（24 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 PO4 PHOSPHATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.3；289 K；25% (w/v) polyethylene glycol 4000, 0.1M Tris-HCl, pH 8.3, 0.2M Li2SO4, vapor diffusion, hanging drop, temperature 289K
|
Resolution 2.00 Å R-free 0.245 |
| 4QQ4 CW-type zinc finger of MORC3 in complex with the amino terminus of histone H3 Deposited 2014-06-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain C
2–16（15 aa）
Fragment：unp residues 2-16
Chain D
2–16（15 aa）
Fragment：unp residues 2-16
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 3 UNX UNKNOWN LIGAND × 7 CL CHLORIDE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；20% PEG-3350, 0.2 M ammonium chloride, vapor diffusion, sitting drop, temperature 293K
|
Resolution 1.75 Å R-free 0.223 |
| 4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
2–12（11 aa）
Fragment：UNP residues 2-12
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate
|
Resolution 2.30 Å R-free 0.229 |
| 4TMP Crystal structure of AF9 YEATS bound to H3K9ac peptide Deposited 2014-06-02 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
2–12（11 aa）
Fragment：UNP residues 2-12
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；291 K；20% PEG4000, 5% 2-Propanol, 0.1 M Sodium Citrate Tribasic Dihydrate
|
Resolution 2.30 Å R-free 0.229 |
| 4U7T Crystal structure of DNMT3A-DNMT3L in complex with histone H3 Deposited 2014-07-31 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain F
2–13（12 aa）
Chain G
2–13（12 aa）
|
Not recorded | ZN ZINC ION × 6 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；0.1M Sodium Acetate, 0.6M Ammonium Sulfate
|
Resolution 2.90 Å R-free 0.261 |
| 4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain C
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, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
|
Resolution 2.60 Å R-free 0.260 |
| 4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain D
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, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
|
Resolution 2.60 Å R-free 0.260 |
| 4W5A Complex structure of ATRX ADD bound to H3K9me3S10ph peptide Deposited 2014-08-17 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
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, SITTING DROP；277 K；13-20% PEG 4000, 0.1 M MES, 3 mM MgCl2
|
Resolution 2.60 Å R-free 0.260 |
| 5B32 The crystal structure of the heterotypic H2AZ/H2A nucleosome with H3.3. Deposited 2016-02-08 | 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 10 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.35 Å R-free 0.259 |
| 5B33 The crystal structure of the H2AZ nucleosome with H3.3. Deposited 2016-02-08 | 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 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.92 Å R-free 0.252 |
| 5BNV Crystal structure of Human MCM2 HBD chaperoning a histone H3-H4 tetramer Deposited 2015-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric（6） Consistent with protein count |
Chain A
58–136（79 aa）
Fragment：UNP residues 58-136
Chain D
58–136（79 aa）
Fragment：UNP residues 58-136
|
Not recorded | PO4 PHOSPHATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；1.5 M sodium/potassium phosphate, pH 8.0
|
Resolution 2.79 Å R-free 0.220 |
| 5BNX Crystal structure of Human MCM2 HBD and ASF1b chaperoning a histone H3.3-H4 dimer Deposited 2015-05-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
58–136（79 aa）
Fragment：UNP residues 58-136
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；3.2 M sodium formate, 0.1 M Tris, pH 8.5
|
Resolution 2.31 Å R-free 0.213 |
| 5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain F
14–31（18 aa）
Fragment：UNP residues 14-31
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
|
Resolution 2.36 Å R-free 0.257 |
| 5DWQ Crystal structure of CARM1, sinefungin, and methylated H3 peptide (R17) Deposited 2015-09-22 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
14–31（18 aa）
Fragment：UNP residues 14-31
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SFG SINEFUNGIN × 2 GOL GLYCEROL × 2 SO4 SULFATE ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
|
Resolution 2.36 Å R-free 0.257 |
| 5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
14–31（18 aa）
Fragment：UNP residues 14-31
Chain G
14–31（18 aa）
Fragment：UNP residues 14-31
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
|
Resolution 2.05 Å R-free 0.263 |
| 5DX0 Crystal structure of CARM1, sinefungin, and H3 peptide (R17) Deposited 2015-09-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain H
14–31（18 aa）
Fragment：UNP residues 14-31
Chain I
14–31（18 aa）
Fragment：UNP residues 14-31
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | SFG SINEFUNGIN × 2 GOL GLYCEROL × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；291 K；0.2 M Ammonium Sulfate, 0.1 M Tris pH 8.5, 18% w/v PEG 3350
|
Resolution 2.05 Å R-free 0.263 |
| 5JA4 Crystal structure of human TONSL and MCM2 HBDs binding to a histone H3-H4 tetramer Deposited 2016-04-11 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain A
58–136（79 aa）
|
Not recorded | MES 2-(N-MORPHOLINO)-ETHANESULFONIC ACID × 2 GOL GLYCEROL × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；298 K；0.1M MES pH 5.6, 7% isopropanol
|
Resolution 2.42 Å R-free 0.246 |
| 5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
30–43（14 aa）
Fragment：H3 peptide, UNP residues 30-43
|
Mutation：K36M | ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
|
Resolution 2.05 Å R-free 0.213 |
| 5JLB Crystal structure of SETD2 bound to histone H3.3 K36I peptide Deposited 2016-04-26 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
30–43（14 aa）
Fragment：H3 peptide, UNP residues 30-43
|
Mutation：K36I | SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 2 ZN ZINC ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；0.2 M KSCN, 0.1 M Bis-Tris Propane, 20% PEG3350
|
Resolution 1.50 Å R-free 0.190 |
| 5KDM Crystal structure of EBV tegument protein BNRF1 in complex with histone chaperone DAXX and histones H3.3-H4 Deposited 2016-06-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；295 K；0.1M MES pH 6.0, 0.8 M ammonium sulfate
|
Resolution 3.50 Å R-free 0.280 |
| 5X7X The crystal structure of the nucleosome containing H3.3 at 2.18 angstrom resolution Deposited 2017-02-27 | 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 | CL CHLORIDE ION × 4 MN MANGANESE (II) ION × 13 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；potassium cacodylate, potassium chloride, manganese chloride
|
Resolution 2.18 Å R-free 0.256 |
| 6A5L RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA Deposited 2018-06-24 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.60 Å |
| 6A5O RNA polymerase II elongation complex stalled at SHL(-6) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.90 Å |
| 6A5P RNA polymerase II elongation complex stalled at SHL(-5) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.00 Å |
| 6A5R RNA polymerase II elongation complex stalled at SHL(-2) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.70 Å |
| 6A5T RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.70 Å |
| 6A5U RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA, tilt conformation Deposited 2018-06-25 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.60 Å |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain E
4–18（15 aa）
|
Mutation：K9R | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain F
4–18（15 aa）
|
Mutation：K9R | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain G
4–18（15 aa）
|
Mutation：K9R | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain H
4–18（15 aa）
|
Mutation：K9R | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6INQ RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome, with foreign DNA (+1 position) Deposited 2018-10-26 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 25-meric（25） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 6IR9 RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome Deposited 2018-11-12 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 6J4W RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-5) of the nucleosome Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.90 Å |
| 6J4X RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1A) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6J4Y RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-1) of the nucleosome (+1B) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.30 Å |
| 6J4Z RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6J50 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome (tilted conformation) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 22 PDB declaration: 27-meric（27） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.70 Å |
| 6J51 RNA polymerase II elongation complex bound with Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome, weak Elf1 (+1 position) Deposited 2019-01-10 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain D
2–27（26 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | FLC CITRATE ANION × 1 ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
|
Resolution 3.01 Å R-free 0.272 |
| 6PZV Crystal Structure of Bovine DNMT1 RFTS domain in complex with H3K9me3 and Ubiquitin Deposited 2019-08-01 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain H
2–27（26 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 3.5；277 K；0.1M citric acid (pH 3.5), 28% PEG8000
|
Resolution 3.01 Å R-free 0.272 |
| 6R0C Human-D02 Nucleosome Core Particle with biotin-streptavidin label Deposited 2019-03-12 | 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 | MN MANGANESE (II) ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 6RNY PFV intasome - nucleosome strand transfer complex Deposited 2019-05-09 | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: octadecameric（18） Consistent with all polymers |
Chain A
1–136（136 aa）
Chain E
1–136（136 aa）
|
Not recorded | MG MAGNESIUM ION × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7
cryo-EM vitrification conditions
Cryogen ETHANE；1 min incubation 3.5s blot
|
Resolution 3.90 Å |
| 6U04 Crystal structure of human BRPF1 PZP bound to histone H3 tail Deposited 2019-08-13 | Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count |
Chain A
2–13（12 aa）
|
Not recorded | PR PRASEODYMIUM ION × 1 ZN ZINC ION × 5 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；291.15 K；0.2 M Lithium sulfate, 0.1 M Tris-HCl pH 8.5, 40% (v/v) PEG400, and 0.01M Praseodymium(III) acetate hydrate
|
Resolution 2.20 Å R-free 0.208 |
| 7A08 CryoEM Structure of cGAS Nucleosome complex Deposited 2020-08-07 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: undecameric（11） Consistent with all polymers |
Chain d
2–136（135 aa）
Chain h
2–136（135 aa）
|
Not recorded | ZN ZINC ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.11 Å |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
58–136（79 aa）
|
Not recorded | SO4 SULFATE ION × 2 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CIZ Crystal structure of DNAJC9 HBD helix2 in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-08 | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain I
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.05 M Lithium sulfate, 0.05 M Sodium sulfate; 0.05 M Tris, pH 8.5, 30% (v/v) PEG400.
|
Resolution 1.80 Å R-free 0.214 |
| 7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain E
58–136（79 aa）
|
Not recorded | GOL GLYCEROL × 1 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.295 |
| 7CJ0 Crystal structure of DNAJC9 HBD in complex with H3.3-H4 dimer and MCM2 HBD Deposited 2020-07-09 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.17 M Sodium acetate, 0.1 M Tris, pH8.5, 25% (v/v) PEG 4000, 20% (v/v) Glycerol
|
Resolution 2.50 Å R-free 0.295 |
| 7CWH Structural basis of RACK7 PHD to read a pediatric glioblastoma-associated histone mutation H3.3G34R Deposited 2020-08-28 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain A
32–42（11 aa）
|
Mutation：G34R | ZN ZINC ION × 2 | SOLUTION NMR |
NMR measurement conditions
pH 7.4；293 K；Ionic strength (raw mmCIF value) 500；Pressure 1
NMR sample composition
0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DDT, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.7 mM [U-13C; U-15N] RACK7 PHD, 1.4 mM H3.3G34R, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 100% D2O | 100% D2O
NMR sample composition
1 mM [U-13C; U-15N] G34R, 1.2 mM RACK7 PHD, 100 mM sodium chloride, 0.02 % w/v sodium azide, 50 mM sodium phosphate, 2 mM [U-2H] DTT, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain E
14–23（10 aa）
Chain F
14–23（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | MLI MALONATE ION × 2 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
|
Resolution 2.20 Å R-free 0.254 |
| 7OKP Crystal structure of mouse CARM1 in complex with histone H3_13-22 K18 acetylated Deposited 2021-05-18 | Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric（8） Consistent with protein count |
Chain G
14–23（10 aa）
Chain H
14–23（10 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | MLI MALONATE ION × 8 QVR (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-[(~{E})-prop-1-enyl]oxolane-3,4-diol × 4 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；1M sodium malonate, 0.1M MES pH7.0, 0.2M sodium chloride
|
Resolution 2.20 Å R-free 0.254 |
| 7V1L Structure of sNASP core in complex with H3 alpha3 helix peptide Deposited 2021-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain V
117–136（20 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；1.4M Na-K phosphate, pH 8.2
|
Resolution 2.85 Å R-free 0.246 |
| 7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
|
Resolution 2.83 Å R-free 0.240 |
| 7V1M Structural basis for the co-chaperone relationship of sNASP and ASF1b Deposited 2021-08-04 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；8% v/v Tacsimate, pH 6.0, 20% w/v PEG 3350
|
Resolution 2.83 Å R-free 0.240 |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain A
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain C
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7VCQ structure of viral protein BKRF4 in complex with H3.3-H4-ASF1 Deposited 2021-09-03 | Assembly 3 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric（3） Consistent with protein count |
Chain G
58–136（79 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2% Tacsimate pH 7.0; o.1M HEPES pH 7.5; 20% PEG3350
|
Resolution 3.00 Å R-free 0.283 |
| 7W5M Crystal structure of AtNASP in complex of H3 alpha3 helix peptide Deposited 2021-11-30 | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric（2） Consistent with protein count |
Chain B
117–136（20 aa）
|
Not recorded | GOL GLYCEROL × 1 PG4 TETRAETHYLENE GLYCOL × 2 SO4 SULFATE ION × 3 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG 300, 0.2M Ammonium sulfate, 0.1M Phosphate citrate, pH 4.2, 10% Glycerol
|
Resolution 2.15 Å R-free 0.227 |
| 7WBV RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-4) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 7WBW RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3.5) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 7.10 Å |
| 7WBX RNA polymerase II elongation complex bound with Elf1 and Spt4/5, stalled at SHL(-3) of the nucleosome Deposited 2021-12-17 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 26-meric（26） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.00 Å |
| 7XSE RNA polymerase II elongation complex transcribing a nucleosome (EC42) Deposited 2022-05-13 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 7XSX RNA polymerase II elongation complex transcribing a nucleosome (EC49) Deposited 2022-05-15 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.80 Å |
| 7XSZ RNA polymerase II elongation complex transcribing a nucleosome (EC115) Deposited 2022-05-15 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 7XT7 RNA polymerase II elongation complex transcribing a nucleosome (EC49B) Deposited 2022-05-16 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.20 Å |
| 7XTD RNA polymerase II elongation complex transcribing a nucleosome (EC58oct) Deposited 2022-05-16 | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric（35） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 7XTI RNA polymerase II elongation complex transcribing a nucleosome (EC58hex) Deposited 2022-05-17 | Assembly 1 Other combination Heteromer；Protein × 30 PDB declaration: 33-meric（33） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.90 Å |
| 8JH2 RNA polymerase II elongation complex bound with Elf1, Spt4/5 and foreign DNA, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 23 PDB declaration: 28-meric（28） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.70 Å |
| 8JH3 RNA polymerase II elongation complex containing 40 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.70 Å |
| 8JH4 RNA polymerase II elongation complex containing 60 bp upstream DNA loop, stalled at SHL(-1) of the nucleosome Deposited 2023-05-22 | Assembly 1 Other combination Heteromer；Protein × 20 PDB declaration: 23-meric（23） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 8 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 50 mM Potassium acetate, 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.20 Å |
| 9B3P The cryo-EM structure of the H2A.Z-H3.3 double-variant nucleosome Deposited 2024-03-19 | 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；20mM Tris-HCl, 5mM NaCl
cryo-EM vitrification conditions
Cryogen ETHANE；Freezing condition: blot force 0, blot time 4.5 second
|
Resolution 3.00 Å |
| 9EOZ Human OGG1 bound to a nucleosome core particle with 8-oxodGuo lesion at SHL6.0 Deposited 2024-03-16 | Assembly 1 Protein–DNA Heteromer；Protein × 9 PDB declaration: 11-meric（11） Consistent with all polymers |
Chain E
2–136（135 aa）
Chain K
2–136（135 aa）
|
Not recorded | No recorded non-water small molecule | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9II7 RNA polymerase II elongation complex stalled at SHL(-1) of the nucleosome containing histone variant H2A.B Deposited 2024-06-19 | Assembly 1 Other combination Heteromer；Protein × 21 PDB declaration: 24-meric（24） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5；20 mM HEPES-KOH(pH7.5), 200 nM Zinc acetate, 0.1 mM TCEP-HCl
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 9J0N Paused elongation complex of mammalian RNA polymerase II with nucleosome (PEC2-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 27 PDB declaration: 30-meric（30） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9J0O Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC1-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric（29） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9J0P Arrested elongation complex of mammalian RNA polymerase II with nucleosome (AEC2-nuc) Deposited 2024-08-02 | Assembly 1 Other combination Heteromer；Protein × 26 PDB declaration: 29-meric（29） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.9
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.30 Å |
| 9L1X hDEK-nucleosome complex (conformation 1) Deposited 2024-12-16 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.69 Å |
| 9L22 hDEK-nucleosome complex (conformation 2) Deposited 2024-12-16 | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: dodecameric（12） Consistent with all polymers |
Chain A
2–136（135 aa）
Chain E
2–136（135 aa）
|
Not recorded | UNX UNKNOWN LIGAND × 2 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.00 Å |
| 9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain B
2–27（26 aa）
Chain D
2–27（26 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
|
Resolution 2.69 Å R-free 0.230 |
| 9UTH DPF3b in complex with H3K14cr peptide Deposited 2025-05-03 | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric（4） Consistent with protein count |
Chain F
2–27（26 aa）
Chain H
2–27（26 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | ZN ZINC ION × 8 | X-RAY DIFFRACTION |
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277.15 K；4 M Sodium Formate, pH 7.0
|
Resolution 2.69 Å R-free 0.230 |
| 9WMS Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type B) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.40 Å |
| 9WMT Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, type A) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.59 Å |
| 9WMU Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type A) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Mutation：K36M Mutation：K36M | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.28 Å |
| 9WMV Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp130, type B) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 13 MG MAGNESIUM ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.66 Å |
| 9WMW Co-transcriptional histone H3K36 methylation complex containing RNA polymerase II elongation complex, Set2, and the upstream nucleosome. (temp115, FACT-hexamer) Deposited 2025-09-03 | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric（34） Consistent with all polymers |
Chain a
1–136（136 aa）
Chain e
1–136（136 aa）
|
Not recorded | ZN ZINC ION × 10 MG MAGNESIUM ION × 1 | ELECTRON MICROSCOPY |
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.62 Å |