7W28: SETD3-SAH

Crystal Structure of SETD3-SAH in complex with betaA-4PyrAla73 peptide. Determined by X-ray diffraction at 1.79 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,596
Mol. weight: 59.71 kDa
Ligands: SAH
Released: 5 Oct 2022

Explore 7W28 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7W28 contains 28 α-helices and 16 β-strands across 2 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, 15 β-strands

Element	Residues	Length	Sheet
α-helix	21-34	14
α-helix	38-40	3
α-helix	45-62	18
α-helix	74-77	4
α-helix	78-87	10
β-strand	95-99	5	1
α-helix	101-103	3
β-strand	105-109	5	1
β-strand	113	1	2
β-strand	118-123	6	3
α-helix	124-126	3
β-strand	128-129	2	4
α-helix	130-134	5
α-helix	139-144	6
α-helix	146-150	5
α-helix	152-164	13
α-helix	172-175	4
α-helix	185-187	3
α-helix	190-194	5
α-helix	202-225	24
α-helix	227-229	3
α-helix	240-253	14
β-strand	255-258	4	4
β-strand	265-269	5	4
α-helix	273-275	3
α-helix	276	1
β-strand	277-278	2	5
β-strand	285-288	4	3
β-strand	293-297	5	3
β-strand	302	1	2
β-strand	307-308	2	1
β-strand	309-310	2	5
α-helix	317-319	3
α-helix	320-324	5
β-strand	335-341	7	6
α-helix	349-359	11
β-strand	364-370	7	6
α-helix	378-388	11
α-helix	391-399	9
α-helix	403-405	3
α-helix	419-439	21
α-helix	444-453	10
α-helix	458-494	37

Chain P: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase setd3	A	protein	499	Homo sapiens	Q86TU7 (AlphaFold model)
Actin, cytoplasmic 1	P	protein	16	Homo sapiens	P60709 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7W28_1 Histone-lysine N-methyltransferase setd3 (chains A)
SMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEK
IRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEEL
FLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTL
PSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSF
TYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVA
LQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLAR
AGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVS
WDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAV
KSAAVNREYYRQQMEEKAP

Sequence of entity 2 (P), FASTA

>7W28_2 Actin, cytoplasmic 1 (chains P)
TLKYPIEXGIVTNWDD

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1

Water and common crystallization additives (SO4) are not listed.

Primary citation

Histidine methyltransferase SETD3 methylates structurally diverse histidine mimics in actin. Hintzen, J.C.J., Ma, H., Deng, H. et al. Protein Sci (2022) 31:e4305-e4305. DOI 10.1002/pro.4305 · 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
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
6ICT 1.95 Å, Structure of SETD3 bound to SAH and methylated actin
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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