6ICT: SETD3

Structure of SETD3 bound to SAH and methylated actin. Determined by X-ray diffraction at 1.95 Å resolution. Released 27 Feb 2019.

Method: X-ray diffraction
Resolution: 1.95 Å
Organism: Homo sapiens
Chains: 8
Atoms: 16,956
Mol. weight: 244.36 kDa
Ligands: SAH
Released: 27 Feb 2019

Explore 6ICT in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6ICT contains 115 α-helices and 67 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	23-37	15
α-helix	46-62	17
α-helix	75-78	4
α-helix	79-88	10
β-strand	96-101	6	1
β-strand	105-110	6	1
β-strand	114	1	2
β-strand	119-124	6	3
α-helix	125-127	3
β-strand	129-130	2	4
α-helix	131-135	5
α-helix	140-145	6
α-helix	147-151	5
α-helix	153-165	13
α-helix	173-176	4
α-helix	186-188	3
α-helix	191-195	5
α-helix	202-226	25
α-helix	228-230	3
α-helix	234-236	3
α-helix	241-254	14
β-strand	256-259	4	4
β-strand	266-270	5	4
α-helix	274-276	3
α-helix	277	1
β-strand	278-279	2	5
β-strand	286-289	4	3
β-strand	294-298	5	3
β-strand	303	1	2
β-strand	308-309	2	1
β-strand	310-311	2	5
α-helix	318-320	3
α-helix	321-325	5
β-strand	336-342	7	6
α-helix	350-359	10
β-strand	365-371	7	6
α-helix	379-388	10
α-helix	392-399	8
α-helix	404-409	6
α-helix	420-438	19
α-helix	445-454	10
β-strand	458	1	7
α-helix	459-494	36
α-helix	497-500	4

Chain B: 28 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	22-37	16
α-helix	39-40	2
α-helix	46-63	18
α-helix	75-78	4
α-helix	79-88	10
β-strand	96-101	6	8
β-strand	105-110	6	8
β-strand	114	1	9
β-strand	119-124	6	10
α-helix	125-127	3
β-strand	129-130	2	11
α-helix	131-135	5
α-helix	140-145	6
α-helix	147-151	5
α-helix	153-165	13
α-helix	173-176	4
α-helix	186-188	3
α-helix	191-195	5
α-helix	202-226	25
α-helix	228-230	3
α-helix	234-236	3
α-helix	241-254	14
β-strand	256-259	4	11
β-strand	266-270	5	11
α-helix	274-276	3
β-strand	278-279	2	12
β-strand	286-289	4	10
β-strand	294-298	5	10
β-strand	303	1	9
β-strand	308-309	2	8
β-strand	310-311	2	12
α-helix	318-320	3
α-helix	321-325	5
β-strand	336-342	7	13
α-helix	350-359	10
β-strand	365-371	7	13
α-helix	379-388	10
α-helix	392-399	8
α-helix	404-409	6
α-helix	420-438	19
α-helix	445-454	10
β-strand	458	1	14
α-helix	459-494	36
α-helix	497-500	4

Chain C: 29 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-37	16
α-helix	39-40	2
α-helix	46-62	17
α-helix	75-78	4
α-helix	79-88	10
β-strand	96-101	6	14
β-strand	105-110	6	14
β-strand	114	1	15
β-strand	119-124	6	16
α-helix	125-127	3
β-strand	129-130	2	17
α-helix	131-135	5
α-helix	140-143	4
α-helix	147-151	5
α-helix	153-165	13
α-helix	173-176	4
α-helix	186-188	3
α-helix	191-195	5
α-helix	202-226	25
α-helix	228-230	3
α-helix	234-236	3
α-helix	241-254	14
β-strand	256-259	4	17
β-strand	266-270	5	17
α-helix	274-276	3
α-helix	277	1
β-strand	278-279	2	18
β-strand	286-289	4	16
β-strand	294-298	5	16
β-strand	303	1	15
β-strand	308-309	2	14
β-strand	310-311	2	18
α-helix	318-320	3
α-helix	321-325	5
β-strand	336-342	7	19
α-helix	350-359	10
β-strand	365-371	7	19
α-helix	379-388	10
α-helix	392-399	8
α-helix	404-409	6
α-helix	420-438	19
α-helix	445-454	10
α-helix	459-494	36
α-helix	497-499	3

Chain D: 28 helices, 15 β-strands

Element	Residues	Length	Sheet
α-helix	22-37	16
α-helix	39-40	2
α-helix	46-63	18
α-helix	75-78	4
α-helix	79-88	10
β-strand	96-101	6	7
β-strand	105-110	6	7
β-strand	114	1	20
β-strand	119-124	6	21
α-helix	125-127	3
β-strand	129-130	2	22
α-helix	131-135	5
α-helix	140-145	6
α-helix	147-151	5
α-helix	153-165	13
α-helix	173-176	4
α-helix	186-188	3
α-helix	191-195	5
α-helix	202-226	25
α-helix	228-230	3
α-helix	234-236	3
α-helix	241-254	14
β-strand	256-259	4	22
β-strand	266-270	5	22
α-helix	274-276	3
α-helix	277	1
β-strand	278-279	2	23
β-strand	286-289	4	21
β-strand	294-298	5	21
β-strand	303	1	20
β-strand	308-309	2	7
β-strand	310-311	2	23
α-helix	318-325	8
β-strand	336-342	7	24
α-helix	350-359	10
β-strand	365-371	7	24
α-helix	379-388	10
α-helix	392-399	8
α-helix	404-409	6
α-helix	420-438	19
α-helix	445-454	10
α-helix	459-494	36
α-helix	497-499	3

Chain E: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	3
α-helix	81-84	4

Chains G and I: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	10

Chain H: 1 helix, 2 β-strands

Element	Residues	Length	Sheet
β-strand	70	1	16
β-strand	73	1	17
α-helix	81-84	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase setd3	A, B, C, D	protein	504	Homo sapiens	Q86TU7 (AlphaFold model)
Actin, cytoplasmic 1	E, G, H, I	protein	23	Homo sapiens	P60709 (AlphaFold model)

Sequence of entity 1 (A, B, C, D), FASTA

>6ICT_1 Histone-lysine N-methyltransferase setd3 (chains A, B, C, D)
GMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEK
IRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEEL
FLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTL
PSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSF
TYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVA
LQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLAR
AGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVS
WDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAV
KSAAVNREYYRQQMEEKAPLPKYE

Sequence of entity 2 (E, G, H, I), FASTA

>6ICT_2 Actin, cytoplasmic 1 (chains E, G, H, I)
TLKYPIEHGIVTNWDDMEKIWHH

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	4

Primary citation

Structural insights into SETD3-mediated histidine methylation on beta-actin. Guo, Q., Liao, S., Kwiatkowski, S. et al. Elife (2019) 8. DOI 10.7554/eLife.43676 · PubMed

Other PDB entries of the same protein (UniProt Q86TU7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6MBK 1.69 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First…
6OX0 1.75 Å, SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor
6WK2 1.76 Å, SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine
6MBJ 1.78 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, P21…
6OX3 1.78 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Lysine
7W28 1.79 Å, Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide
6WK1 1.89 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine
6OX1 1.95 Å, SETD3 in Complex with an Actin Peptide with Target Histidine Partially Methylated
6V63 2.02 Å, SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine
3SMT 2.04 Å, Crystal structure of human SET domain-containing protein3
6OX2 2.09 Å, SETD3in Complex with an Actin Peptide with the Target Histidine Fully Methylated
6OX5 2.1 Å, A SETD3 Mutant (N255A) in Complex with an Actin Peptide with His73 Replaced with Lysine

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