6v62

SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine

Method: X-RAY DIFFRACTION D_max: 84.4 Å Quality: EXCELLENT

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

Actin, cytoplasmic 1

OrganismNot specified

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 Y； UniProt 66–88	Mutation：H73K	Actin-histidine N-methyltransferase × 1 （Q86TU7） 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

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 6V62	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
6OX3 SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine Deposited 2019-05-13	Different construct Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 66–84（19 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 mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 66–84（19 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
6V63 SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine Deposited 2019-12-04	Different mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Y 66–88（23 aa）	Mutation：H73Q	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 mutation/modification Different ligand/ion Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain Z 66–88（23 aa）	Mutation：H73Q	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

2 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	C9JUM1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Y； PDBConstruct 1–23； UniProt 66–88

Actin-histidine N-methyltransferase

Homo sapiens

UniProt Q86TU7

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 1–594	Mutation：N255F, W273A	Actin, cytoplasmic 1 × 1 （C9JUM1） 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

Other States of the Same Protein in the Database

Other PDB	Difference from Current Entry 6V62	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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–503（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–503（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 mutation/modification 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 mutation/modification 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–503（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–503（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
6JAT Crystal structure of SETD3 bound to Actin peptide and SFG Deposited 2019-01-25	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 1–498（498 aa） Fragment：SETD3 protein	Not recorded	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
6JAT Crystal structure of SETD3 bound to Actin peptide and SFG Deposited 2019-01-25	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 C 1–498（498 aa） Fragment：SETD3 protein	Not recorded	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
6MBJ SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21 Crystal Form Deposited 2018-08-30	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）	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 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）	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 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）	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 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）	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 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）	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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 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）	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 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）	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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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
6V63 SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine Deposited 2019-12-04	Different mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 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 mutation/modification Different ligand/ion 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 mutation/modification Different ligand/ion 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 mutation/modification 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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–498（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 mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–498（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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 42 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SETD3_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain A； PDBConstruct 3–596； UniProt 1–594

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	6v62
Deposition date deposition_date	2019-12-04
Structure title title	SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine
Keywords keywords	TRANSFERASE, TRANSFERASE-STRUCTURAL PROTEIN complex; TRANSFERASE/STRUCTURAL PROTEIN
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	26.79 Å
Radius of gyration Rg (electron density) rg_electron	25.89 Å
Forward intensity I(0) i0	52034700.00
Molecular weight molecular_weight	56844.0 kDa
Excluded volume excluded_volume	71361 Å³
Envelope volume envelope_volume	87984 Å³
Hydration-shell volume shell_volume	28571 Å³
Envelope diameter envelope_diameter	87.2 Å
Shell Rg shell_rg	32.76 Å
Envelope Rg envelope_rg	26.04 Å
Shape Rg shape_rg	25.88 Å
Total Rg total_rg	26.67 Å
Total atoms total_atoms	4010
Residues n_residues	502
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	84.4 Å
Rg (real space) rg_real	26.77 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	5.2030e+07
I(0) uncertainty (real space) i0_real_error	6.7670e+05
Rg (reciprocal space) rg_reciprocal	26.78 Å
I(0) (reciprocal space) i0_reciprocal	52040000.0000
Solution quality estimate total_estimate	0.9052
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.6 Å
Skewness Skewness skewness	0.288
Kurtosis Kurtosis kurtosis	-0.499
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	13730000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.945; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.983; Smooth: 0.945

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Actin, cytoplasmic 1
Molecular weight formula_weight	2859.3 kDa
Mutation mutation	H73K
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Y
Atom count atom_count	4213

TLKYPIEKGIVTNWDDMEKIWHH

Entity 2 Entity 2 polymer

Description description	Actin-histidine N-methyltransferase
Molecular weight formula_weight	67404.1 kDa
EC 编号 ec_number	2.1.1.85
Mutation mutation	N255F, W273A
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A

GSMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFTYEDYRWAVSSVMTRQFQIPTEDGSRVTLALIPLADMCNHTNGLITTGYNLEDDRCECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVKSAAVNREYYRQQMEEKAPLPKYEESNLGLLESSVGDSRLPLVLRNLEEEAGVQDALNIREAISKAKATENGLVNGENSIPNGTRSENESLNQESKRAVEDAKGSSSDSTAGVKE

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 3 Entity 3 non-polymer

Description description	S-ADENOSYL-L-HOMOCYSTEINE
Molecular weight formula_weight	384.4 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	187

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8. Citations (1)

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Unit-cell length a length_a	60.654 Å
Unit-cell length b length_b	116.752 Å
Unit-cell length c length_c	174.377 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	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	orthorhombic

Resolution resolution	2.360 Å
Low-resolution limit resolution_low	39.490 Å
R factor r_factor	0.2102
R_work r_work	0.2080
R_free r_free	0.2524

fit	/app/data/saxs_computation/v6/6v62/6v62.fit
pddf	/app/data/pr_computation/v6/6v62/6v62.pr.out
profile	/app/data/saxs_computation/v6/6v62/6v62.dat

SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced with Lysine

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

Actin, cytoplasmic 1

State in the Current Structure

Other States of the Same Protein in the Database

Actin-histidine N-methyltransferase

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 (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)