Histone-lysine N-methyltransferase SETD2
Homo sapiens
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 1433–1711 | Not recorded | ALA-PRO-ARG-PHE-GLY-GLY-VAL-MET-ARG-PRO-ASN-ARG × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 UNX UNKNOWN LIGAND × 20 ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；291 K；0.2 M KSCN, 0.1 M Tris-HCl pH 8.5, and 26% PEG 3350 | Resolution 2.30 Å R-free 0.263 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 6VDB | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2A7O Solution Structure of the hSet2/HYPB SRI domain Deposited 2005-07-05 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1954–2061（108 aa）
Fragment：Set2 Rpb1-interacting (SRI) domain, HSET2/HYBP SRI domain, residues 1954-2061
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；300 K；Ionic strength (raw mmCIF value) 100 mM KCl；Pressure ambient
NMR sample composition
U-15N (random labeling) HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
U-95% 13C, U-98% 15N labeled HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
Residue selective labeling with 15N-lysine HYPB, 90% H2O, 10% D2O | 90% H2O/10% D2O
NMR sample composition
U-95% 13C, U-98% 15N HYPB, 100% D2O | 100% D2O
NMR sample composition
Unlabeled HYPB,100% D2O | 100% D2O
NMR sample composition
10% 13C (fractional labeling) HYPB,100% D2O | 100% D2O
|
Resolution not provided |
| 2MDC Solution structure of the WW domain of HYPB Deposited 2013-09-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2385–2430（46 aa）
Fragment：UNP residues 2385- 2430
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition
500 mM [U-99% 13C; U-99% 15N] H2O-1, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2MDI Solution structure of the PP2WW mutant (KPP2WW) of HYPB Deposited 2013-09-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2377–2430（54 aa）
Fragment：UNP residues 2377-2430
|
Mutation：K11A, P12A, K13A | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition
500 uM [U-99% 13C; U-99% 15N] KPP2WW-1, 20 mM sodium phosphate-2, 50 mM sodium chloride-3, 5%(w/v) sodium azide-4, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 2MDJ Solution structure of WW domain with polyproline stretch (PP2WW) of HYPB Deposited 2013-09-11 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2377–2430（54 aa）
Fragment：UNP residues 2377-2430
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 0.08；Pressure ambient
NMR sample composition
500uM [U-99% 13C; U-99% 15N] PP2WW-1, 20mM sodium phosphate-2, 50mM sodium chloride-3, 0.05%(w/v) sodium azide-4, 95% H2O/5% D2O | 95% H2O/5% D2O
|
Resolution not provided |
| 4FMU Crystal structure of Methyltransferase domain of human SET domain-containing protein 2 Compound: Pr-SNF Deposited 2012-06-18 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 0UM (2S,5S)-2-amino-6-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]-5-(propylamino)hexanoic acid × 1 UNX UNKNOWN LIGAND × 13 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% PEG4000, 10% isoprpanol, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.235 |
| 4H12 The crystal structure of methyltransferase domain of human SET domain-containing protein 2 in complex with S-adenosyl-L-homocysteine Deposited 2012-09-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
Fragment：methyltransferase domain (UNP residues 1434-1711)
|
Not recorded | ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；298 K；1 uL protein (1:10 molar ratio of SETD2:AdoMet) + 1 uL reservoir solution (30% PEG2000 MME, 0.1 M potassium thiocyanate), VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.06 Å R-free 0.249 |
| 5JJY Crystal structure of SETD2 bound to histone H3.3 K36M peptide Deposited 2016-04-25 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1434–1711（278 aa）
Fragment：catalytic domain, UNP residues 1434-1711
|
Not recorded | 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 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1434–1711（278 aa）
Fragment：catalytic domain, UNP residues 1434-1711
|
Not recorded | 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 |
| 5JLE Crystal structure of SETD2 bound to SAH Deposited 2016-04-27 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
Fragment：catalytic domain, UNP residues 1434-1711
|
Not recorded | ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；291 K；0.1 M KSCN, 30% PEG2000mme
|
Resolution 2.40 Å R-free 0.250 |
| 5LSS Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76H [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-propyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1M KSCN, 31.0%w/v PEG 3350, 0.1M HEPES/NaOHpH=7
|
Resolution 1.79 Å R-free 0.226 |
| 5LSX Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 76O [(2~{R},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(phenylmethyl)azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, pH 7.3, 0.1MKSCN, 25-30%MPEG2000
|
Resolution 2.90 Å R-free 0.280 |
| 5LSY Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76M [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(2-methylpropyl)azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000
|
Resolution 1.62 Å R-free 0.215 |
| 5LSZ Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-05 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76K [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-(3-oxidanylpropyl)azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes pH7.3, 0.1MKSCN, 25-30%MPEG2000
|
Resolution 1.62 Å R-free 0.201 |
| 5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.
|
Resolution 2.05 Å R-free 0.231 |
| 5LT6 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 1 76J [(2~{S},5~{S})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-pentyl-azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1MHepes,pH7.3, 0.1MKSCN, 25-30%MPEG2000.
|
Resolution 2.05 Å R-free 0.231 |
| 5LT7 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
|
Not recorded | ZN ZINC ION × 3 SCN THIOCYANATE ION × 2 76L [(2~{S},5~{R})-1-[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]-5-azaniumyl-6-oxidanyl-6-oxidanylidene-hexan-2-yl]-[(2~{R})-2-oxidanylpropyl]azanium × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes, PH7.3, 0.1MKSCN, 25-30%MPEG2000
|
Resolution 1.51 Å R-free 0.192 |
| 5LT8 Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin Derivatives Deposited 2016-09-06 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1433–1711（279 aa）
|
Not recorded | ZN ZINC ION × 3 SFG SINEFUNGIN × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES, PH7.3, 0.1MKSCN, 25-30%MPEG2000
|
Resolution 1.57 Å R-free 0.216 |
| 5V21 Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAM Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1435–1711（277 aa）
Fragment：SET domain (UNP residues 1435-1711)
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME
|
Resolution 2.42 Å R-free 0.269 |
| 5V22 Crystal structure of human SETD2 SET-domain in complex with H3K36M peptide and SAH Deposited 2017-03-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1435–1711（277 aa）
Fragment：SET domain (UNP residues 1435-1711)
|
Not recorded | ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M KSCN, 24% (v/v) PEG 2000 MME
|
Resolution 2.40 Å R-free 0.257 |
| 6J9J crystal structure of SESTD2 in complex with H3.3S31phK36M peptide Deposited 2019-01-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1447–1703（257 aa）
|
Not recorded | ZN ZINC ION × 3 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SCN THIOCYANATE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M potassium thiocyanate, 0.1M Bis-Tris propane,20% PEG 3350
|
Resolution 1.78 Å R-free 0.206 |
| 7EA8 Human SETD2 bound to a nucleosome containing oncohistone mutations Deposited 2021-03-06 | Different construct 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 L
1452–1696（245 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2167–2192（26 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5
|
Resolution 1.80 Å R-free 0.198 |
| 7EVR Crystal structure of hnRNP L RRM2 in complex with SETD2 Deposited 2021-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2167–2192（26 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.8M Potassium/Sodium phosphate, pH 7.5
|
Resolution 1.80 Å R-free 0.198 |
| 7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
2180–2192（13 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000
|
Resolution 1.60 Å R-free 0.204 |
| 7EVS Crystal structure of hnRNP LL RRM2 in complex with SETD2 Deposited 2021-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
2180–2192（13 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.3M Ammonium Sulfate, 20% PEG 4000
|
Resolution 1.60 Å R-free 0.204 |
| 7LZB Crystal Structure of SETD2 bound to Compound 2 Deposited 2021-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YJ1 N-[(1r,4r)-4-(beta-alanylamino)cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 BME BETA-MERCAPTOETHANOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1M Tris pH 7.8, 25% w/v PEG 2000 MME
|
Resolution 2.28 Å R-free 0.264 |
| 7LZD Crystal Structure of SETD2 bound to Compound 35 Deposited 2021-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHY N-{3-[4-(dimethylamino)piperidin-1-yl]phenyl}-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 9 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES pH 7.5, 24% w/v PEG 2000 MME
|
Resolution 1.80 Å R-free 0.218 |
| 7LZF Crystal Structure of SETD2 bound to Compound 57 Deposited 2021-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 YHV 4-fluoro-N-[(1R,3S)-3-{(3S)-3-[(methanesulfonyl)(methyl)amino]pyrrolidin-1-yl}cyclohexyl]-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
|
Resolution 2.47 Å R-free 0.263 |
| 7TY2 Crystal Structure of SETD2 Bound to an Indole-based Inhibitor Deposited 2022-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KS6 N-[(1R,3S)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M HEPES 7.5, 18% w/v PEG 2000 MME
|
Resolution 2.44 Å R-free 0.270 |
| 7TY3 Crystal Structure of SETD2 Bound to an Indole-based Inhibitor Deposited 2022-02-11 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1434–1711（278 aa）
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 KRF N-[(1R,3R)-3-(4-acetylpiperazin-1-yl)cyclohexyl]-4-fluoro-7-methyl-1H-indole-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Potassium thiocyanate, 0.1 M Tris pH 7.5, 18% w/v PEG 2000 MME
|
Resolution 2.30 Å R-free 0.270 |
| 8Q5P Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from human tyrosine kinase ACK1 Deposited 2023-08-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1433–1711（279 aa）
Fragment：UNP residues 1433-1711
|
Not recorded | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.1M TRIS pH 8.5, 16%w/v PEG 10000
|
Resolution 1.81 Å R-free 0.246 |
| 8RZU Structure of human SETD2 L1609P mutant in complex with SAM and H3K36M peptide Deposited 2024-02-13 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1433–1711（279 aa）
|
Mutation：L1609P | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl, pH 8.5
|
Resolution 2.19 Å R-free 0.264 |
| 9EGZ RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, bp +27 Deposited 2024-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain l
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 12 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.90 Å |
| 9EH0 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 30 bp upstream Deposited 2024-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain l
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.60 Å |
| 9EH1 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-nucleosome, 20 bp upstream Deposited 2024-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain l
1452–2040（589 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9EH2 RNA polymerase II-DSIF-SPT6-PAF1c-TFIIS-IWS1-SETD2-FACT nucleosome upstream Deposited 2024-11-21 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain l
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.10 Å |
| 9G4A Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide Deposited 2024-07-15 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1433–1711（279 aa）
|
Mutation：T1663M | ZN ZINC ION × 3 SAM S-ADENOSYLMETHIONINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；32% w/v PEG 4K, 100mM Tris, 800mM LiCl
|
Resolution 1.65 Å R-free 0.241 |
| 9GW2 State 2 MAP 1 SETD2 bound to proximal H3 of upstream nucleosome Deposited 2024-09-26 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain O
1435–2564（1130 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.84 Å |
| 9HGG SETD2 peptide bound to SPOP MATH domain Deposited 2024-11-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1363–1379（17 aa）
|
Not recorded | MG MAGNESIUM ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；10% w/v PEG 20 000, 20% v/v PEG MME 550, 0.03 M sodium fluoride, 0.03 M sodium bromide, 0.1 M MES/imidazole pH 6.5
|
Resolution 1.90 Å R-free 0.256 |
| 9RTN State 2 MAP 2 SPT6 with SETD2 Deposited 2025-07-03 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain O
1435–2564（1130 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.82 Å |
| 9RZC State 3 MAP 1 SETD2 bound to distal H3 of upstream nucleosome Deposited 2025-07-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 10 PDB declaration: 12-meric |
Chain O
1435–2564（1130 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.66 Å |
| 9RZD State 3 MAP 2 SPT6 with SETD2 Deposited 2025-07-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain O
1435–2564（1130 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.69 Å |
| 9RZE State 2 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to proximal upstream H3 Deposited 2025-07-15 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain O
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 8.53 Å |
| 9S0U State 3 MAP 3 RNA Pol II activated elongation complex with SETD2 bound to distal upstream H3 Deposited 2025-07-17 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 32 PDB declaration: 35-meric |
Chain O
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.72 Å |
| 9S3G State 1 MAP3 RNA Pol II activated elongation complex with SETD2 and upstream hexasome Deposited 2025-07-24 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 31 PDB declaration: 34-meric |
Chain O
1435–2564（1130 aa）
|
Not recorded | ZN ZINC ION × 9 MG MAGNESIUM ION × 1 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.4
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.40 Å |
42 other PDB entries and 45 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | SETD2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 17–295； UniProt 1433–1711 |