6jat

Crystal structure of SETD3 bound to Actin peptide and SFG

Method: X-RAY DIFFRACTION D_max: 117.4 Å Quality: GOOD

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

Histone-lysine N-methyltransferase setd3

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 1–498	Fragment：SETD3 protein	Actin, gamma-enteric smooth muscle × 1 （P63267） SFG SINEFUNGIN × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol	Resolution 2.71 Å R-free 0.243
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–498	Fragment：SETD3 protein	Actin, gamma-enteric smooth muscle × 1 （P63267） SFG SINEFUNGIN × 1 SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol	Resolution 2.71 Å R-free 0.243

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 6JAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3SMT Crystal structure of human SET domain-containing protein3 Deposited 2011-06-28	Different construct Different mutation/modification 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 2–498（497 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 1 ARS ARSENIC × 2 PG4 TETRAETHYLENE GLYCOL × 1 ACT ACETATE ION × 2 UNX UNKNOWN LIGAND × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；20 % PEG4000, 0.2 M calcium Acetate, 0.1 M sodium cacodalyte, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.04 Å R-free 0.259
3SMT Crystal structure of human SET domain-containing protein3 Deposited 2011-06-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–498（497 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	SAM S-ADENOSYLMETHIONINE × 2 ARS ARSENIC × 4 PG4 TETRAETHYLENE GLYCOL × 2 ACT ACETATE ION × 4 UNX UNKNOWN LIGAND × 22	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；297 K；20 % PEG4000, 0.2 M calcium Acetate, 0.1 M sodium cacodalyte, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.04 Å R-free 0.259
6ICT Structure of SETD3 bound to SAH and methylated actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Magnesium acetate tetrahydrate 0.1M Sodium cacodylate trihydrate pH 6.5 20% Polyethylene glycol 8000	Resolution 1.95 Å R-free 0.214
6ICT Structure of SETD3 bound to SAH and methylated actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Magnesium acetate tetrahydrate 0.1M Sodium cacodylate trihydrate pH 6.5 20% Polyethylene glycol 8000	Resolution 1.95 Å R-free 0.214
6ICT Structure of SETD3 bound to SAH and methylated actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Magnesium acetate tetrahydrate 0.1M Sodium cacodylate trihydrate pH 6.5 20% Polyethylene glycol 8000	Resolution 1.95 Å R-free 0.214
6ICT Structure of SETD3 bound to SAH and methylated actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.2M Magnesium acetate tetrahydrate 0.1M Sodium cacodylate trihydrate pH 6.5 20% Polyethylene glycol 8000	Resolution 1.95 Å R-free 0.214
6ICV Structure of SETD3 bound to SAH and unmodified actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M HEPES sodium pH 7.5 2% Polyethylene glycol 400 2.0M Ammonium sulfate	Resolution 2.15 Å R-free 0.205
6ICV Structure of SETD3 bound to SAH and unmodified actin Deposited 2018-09-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–503（503 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；291 K；0.1M HEPES sodium pH 7.5 2% Polyethylene glycol 400 2.0M Ammonium sulfate	Resolution 2.15 Å R-free 0.205
6MBJ SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form Deposited 2018-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 19 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；292 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000	Resolution 1.78 Å R-free 0.223
6MBJ SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form Deposited 2018-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 16 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.6；292 K；0.2 M Ammonium acetate, 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 30% w/v Polyethylene glycol 4,000	Resolution 1.78 Å R-free 0.223
6MBK SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First P212121 Crystal Form Deposited 2018-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 6 GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.69 Å R-free 0.243
6MBK SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First P212121 Crystal Form Deposited 2018-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 1.69 Å R-free 0.243
6MBL SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second P212121 Crystal Form Deposited 2018-08-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.5；292 K；0.2 M Sodium chloride, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350	Resolution 2.20 Å R-free 0.227
6OX0 SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	SFG SINEFUNGIN × 1 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.75 Å R-free 0.225
6OX0 SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SFG SINEFUNGIN × 1 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.75 Å R-free 0.225
6OX1 SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.95 Å R-free 0.201
6OX1 SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.95 Å R-free 0.201
6OX2 SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.09 Å R-free 0.239
6OX2 SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 8 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.09 Å R-free 0.239
6OX3 SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	GOL GLYCEROL × 5 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 22 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.78 Å R-free 0.246
6OX3 SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine Deposited 2019-05-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 12 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.78 Å R-free 0.246
6OX4 A SETD3 Mutant (N255A) in Complex with an Actin Peptide Deposited 2019-05-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Mutation：N255A	EDO 1,2-ETHANEDIOL × 17 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 GOL GLYCEROL × 3 ACT ACETATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.29 Å R-free 0.236
6OX4 A SETD3 Mutant (N255A) in Complex with an Actin Peptide Deposited 2019-05-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Mutation：N255A	EDO 1,2-ETHANEDIOL × 15 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.29 Å R-free 0.236
6OX5 A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine Deposited 2019-05-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Mutation：N255A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.10 Å R-free 0.205
6V62 SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine Deposited 2019-12-04	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Mutation：N255F, W273A	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.36 Å R-free 0.252
6V63 SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine Deposited 2019-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	GOL GLYCEROL × 2 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 20 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.02 Å R-free 0.199
6V63 SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine Deposited 2019-12-04	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 EDO 1,2-ETHANEDIOL × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 2.02 Å R-free 0.199
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–594（594 aa） Chain B 1–594（594 aa）	Not recorded	GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 46 SAH S-ADENOSYL-L-HOMOCYSTEINE × 2 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	GOL GLYCEROL × 6 EDO 1,2-ETHANEDIOL × 27 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK1 SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	EDO 1,2-ETHANEDIOL × 19 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.89 Å R-free 0.228
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–594（594 aa） Chain D 1–594（594 aa）	Mutation：N255V Mutation：N255V	SAM S-ADENOSYLMETHIONINE × 2 EDO 1,2-ETHANEDIOL × 8 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Mutation：N255V	SAM S-ADENOSYLMETHIONINE × 1 EDO 1,2-ETHANEDIOL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
6WK2 SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine Deposited 2020-04-15	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–594（594 aa）	Mutation：N255V	SAM S-ADENOSYLMETHIONINE × 1 EDO 1,2-ETHANEDIOL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.6；292 K；0.2 M ammonium acetate, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 30% (w/v) polyethylene glycol 4000	Resolution 1.76 Å R-free 0.206
7LMS Structure of human SetD3 methyl-transferase in complex with 2A protease from Coxsackievirus B3 Deposited 2021-02-05	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 2–594（593 aa）	Not recorded	ZN ZINC ION × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 7.2 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.50 Å
7W28 Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide Deposited 2021-11-22	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–498（498 aa） Fragment：SETD3	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；289 K；30%(w/v) PEG4000, 0.1 M Tris base/Hydrochloric acid 8.5, 0.2M Lithium sulfate.	Resolution 1.79 Å R-free 0.211
7W29 Crystal Structure of SETD3-SAH in complex with betaA-Orn73 peptide Deposited 2021-11-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–498（498 aa） Fragment：SETD3	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9；289 K；20%(w/v) PEG6000, 0.1M Bicine/Sodium hydroxide 9.0	Resolution 2.90 Å R-free 0.279
8X77 Enterovirus proteinase with host factor Deposited 2023-11-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.02M Citric acid, 0.08M BIS-TRIS propane, pH8.8, 16% PEG 3350	Resolution 3.52 Å R-free 0.291
8X77 Enterovirus proteinase with host factor Deposited 2023-11-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 1–594（594 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.02M Citric acid, 0.08M BIS-TRIS propane, pH8.8, 16% PEG 3350	Resolution 3.52 Å R-free 0.291
8X77 Enterovirus proteinase with host factor Deposited 2023-11-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain G 1–594（594 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.02M Citric acid, 0.08M BIS-TRIS propane, pH8.8, 16% PEG 3350	Resolution 3.52 Å R-free 0.291
8X77 Enterovirus proteinase with host factor Deposited 2023-11-23	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–594（594 aa）	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；296 K；0.02M Citric acid, 0.08M BIS-TRIS propane, pH8.8, 16% PEG 3350	Resolution 3.52 Å R-free 0.291
8X8Q Structure of enterovirus protease in complex host factor Deposited 2023-11-28	Different construct Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–594（594 aa）	Not recorded	ZN ZINC ION × 1	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.14 Å

21 other PDB entries and 41 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SETD3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–499； UniProt 1–498 Author chain C； PDBConstruct 2–499； UniProt 1–498

Actin, gamma-enteric smooth muscle

OrganismNot specified

UniProt P63267

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 B； UniProt 61–82	Fragment：Actin peptide	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） SFG SINEFUNGIN × 1 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol	Resolution 2.71 Å R-free 0.243
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain D； UniProt 61–82	Fragment：Actin peptide	Histone-lysine N-methyltransferase setd3 × 1 （Q86TU7） SFG SINEFUNGIN × 1 SO4 SULFATE ION × 2 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；0.2 M HEPES/Sodium hydroxide, 0.2 M Ammonium sulfate, 20% PEG 8000, 10% 2-propanol	Resolution 2.71 Å R-free 0.243

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6JAT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
8V2O Cryo-EM Structure of Wildtype Smooth Muscle Gamma Actin (ACTG2) Deposited 2023-11-23	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–376（376 aa） Chain B 1–376（376 aa） Chain C 1–376（376 aa） Chain D 1–376（376 aa） Chain E 1–376（376 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Actin F-buffer cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: 0 Blot Time: 2.5 s	Resolution 2.45 Å
8V2Z Cryo-EM Structure of Smooth Muscle Gamma Actin (ACTG2) Mutant R257C Deposited 2023-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 5 PDB declaration: pentameric	Chain A 1–376（376 aa） Chain B 1–376（376 aa） Chain C 1–376（376 aa） Chain D 1–376（376 aa） Chain E 1–376（376 aa）	Mutation：R257C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R257C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R257C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R257C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R257C Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Actin F-buffer cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: 0 Blot Time: 2.5 s	Resolution 2.72 Å
8V30 Smooth Muscle Gamma Actin (ACTG2) Filament Mutant R40C Deposited 2023-11-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 10 PDB declaration: decameric	Chain A 1–376（376 aa） Chain B 1–376（376 aa） Chain C 1–376（376 aa） Chain D 1–376（376 aa） Chain E 1–376（376 aa）	Mutation：R40C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R40C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R40C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R40C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：R40C Non-standard monomer：Yes (specific site not provided by mmCIF)	ADP ADENOSINE-5'-DIPHOSPHATE × 5 MG MAGNESIUM ION × 5	ELECTRON MICROSCOPY cryo-EM buffer pH 8；Actin F-buffer cryo-EM vitrification conditions Cryogen ETHANE；Blot Force: 0 Blot Time: 2.5 s	Resolution 2.54 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ACTH_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–22； UniProt 61–82 Author chain D； PDBConstruct 1–22； UniProt 61–82

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	6jat
Deposition date deposition_date	2019-01-25
Structure title title	Crystal structure of SETD3 bound to Actin peptide and SFG
Keywords keywords	SET domain, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	34.54 Å
Radius of gyration Rg (electron density) rg_electron	34.16 Å
Forward intensity I(0) i0	199670000.00
Molecular weight molecular_weight	114230.0 kDa
Excluded volume excluded_volume	143210 Å³
Envelope volume envelope_volume	183200 Å³
Hydration-shell volume shell_volume	45471 Å³
Envelope diameter envelope_diameter	126.4 Å
Shell Rg shell_rg	39.72 Å
Envelope Rg envelope_rg	34.67 Å
Shape Rg shape_rg	34.12 Å
Total Rg total_rg	34.72 Å
Total atoms total_atoms	8051
Residues n_residues	978
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	117.4 Å
Rg (real space) rg_real	34.62 Å
Rg uncertainty (real space) rg_real_error	1.02 Å
I(0) (real space) i0_real	1.9970e+08
I(0) uncertainty (real space) i0_real_error	3.3800e+06
Rg (reciprocal space) rg_reciprocal	34.57 Å
I(0) (reciprocal space) i0_reciprocal	199700000.0000
Solution quality estimate total_estimate	0.8688
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	40.8 Å
Skewness Skewness skewness	0.474
Kurtosis Kurtosis kurtosis	-0.098
Angular range angular_range	— – 0.2300 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	36610000.0000
Real-space data points n_real_points	47
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.993; Smooth: 0.934

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Histone-lysine N-methyltransferase setd3
Molecular weight formula_weight	57223.0 kDa
EC 编号 ec_number	2.1.1.43
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8135

SMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVKSAAVNREYYRQQMEEKAP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	Human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Actin, gamma-enteric smooth muscle
Molecular weight formula_weight	2573.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

SKRGILTLKYPIEHGIITNWDD

Entity 3 Entity 3 non-polymer

Description description	SINEFUNGIN
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 non-polymer

Description description	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
Molecular weight formula_weight	238.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	84

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8. Citations (1)

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Unit-cell length a length_a	60.434 Å
Unit-cell length b length_b	131.282 Å
Unit-cell length c length_c	175.153 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.713 Å
Low-resolution limit resolution_low	49.740 Å
R factor r_factor	0.2018
R_work r_work	0.1995
R_free r_free	0.2429

fit	/app/data/saxs_computation/ja/6jat/6jat.fit
pddf	/app/data/pr_computation/ja/6jat/6jat.pr.out
profile	/app/data/saxs_computation/ja/6jat/6jat.dat

Crystal structure of SETD3 bound to Actin peptide and SFG

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

Histone-lysine N-methyltransferase setd3

State in the Current Structure

Other States of the Same Protein in the Database

Actin, gamma-enteric smooth muscle

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)