6MBK: SETD3, a Histidine Methyltransferase

SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, First P212121 Crystal Form. Determined by X-ray diffraction at 1.69 Å resolution. Released 19 Dec 2018.

Method: X-ray diffraction
Resolution: 1.69 Å
Organism: Homo sapiens
Chains: 4
Atoms: 9,190
Mol. weight: 141.47 kDa
Ligands: SAH
Released: 19 Dec 2018

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

Secondary structure: helices and β-sheets

6MBK contains 57 α-helices and 34 β-strands across 4 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	21-35	15
α-helix	38-39	2
α-helix	42-44	3
α-helix	45-61	17
α-helix	74-77	4
α-helix	78-87	10
β-strand	95-100	6	2
β-strand	104-109	6	2
β-strand	113	1	3
β-strand	118-123	6	1
α-helix	124-126	3
β-strand	128-129	2	4
α-helix	130-134	5
α-helix	139-142	4
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	1
β-strand	293-297	5	1
β-strand	302	1	3
β-strand	307-308	2	2
β-strand	309-310	2	5
α-helix	317-324	8
β-strand	335-341	7	6
α-helix	349-358	10
β-strand	364-370	7	6
α-helix	378-387	10
α-helix	391-398	8
α-helix	403-408	6
α-helix	419-437	19
α-helix	444-453	10
β-strand	457	1	7
α-helix	458-494	37
α-helix	496-499	4

Chain B: 29 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	21-35	15
α-helix	38-39	2
α-helix	42-44	3
α-helix	45-61	17
α-helix	74-77	4
α-helix	78-87	10
β-strand	95-100	6	7
β-strand	104-109	6	7
β-strand	113	1	9
β-strand	118-123	6	8
α-helix	124-126	3
β-strand	128-129	2	10
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	233-235	3
α-helix	240-253	14
β-strand	255-258	4	10
β-strand	265-269	5	10
α-helix	273-275	3
α-helix	276	1
β-strand	277-278	2	11
β-strand	285-288	4	8
β-strand	293-297	5	8
β-strand	302	1	9
β-strand	307-308	2	7
β-strand	309-310	2	11
α-helix	317-324	8
β-strand	335-341	7	12
α-helix	349-359	11
β-strand	364-370	7	12
α-helix	378-387	10
α-helix	391-398	8
α-helix	403-408	6
α-helix	419-437	19
α-helix	444-453	10
β-strand	457	1	2
α-helix	458-494	37
α-helix	496-499	4

Chains Y and Z: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin peptide	Y, Z	protein	15	Homo sapiens	P60709 (AlphaFold model)
Histone-lysine N-methyltransferase setd3	A, B	protein	599	Homo sapiens	Q86TU7 (AlphaFold model)

Sequence of entity 1 (Y, Z), FASTA

>6MBK_1 Actin peptide (chains Y, Z)
TLKYPIEHGIVTNWD

Sequence of entity 2 (A, B), FASTA

>6MBK_2 Histone-lysine N-methyltransferase setd3 (chains A, B)
GPLGSMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRT
LVEKIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIK
AEELFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPY
IQTLPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPL
KDSFTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRC
ECVALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAE
VLARAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSE
FPVSWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEIL
EKAVKSAAVNREYYRQQMEEKAPLPKYEESNLGLLESSVGDSRLPLVLRNLEEEAGVQDA
LNIREAISKAKATENGLVNGENSIPNGTRSENESLNQESKRAVEDAKGSSSDSTAGVKE

Ligands and cofactors

ID	Name	Formula	Copies
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	2

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

Primary citation

SETD3 is an actin histidine methyltransferase that prevents primary dystocia. Wilkinson, A.W., Diep, J., Dai, S. et al. Nature (2019) 565:372-376. DOI 10.1038/s41586-018-0821-8 · PubMed

Other PDB entries of the same protein (UniProt P60709 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6OX0 1.75 Å, SETD3 in Complex with an Actin Peptide with Sinefungin Replacing SAH as Cofactor
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
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
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
6ICV 2.15 Å, Structure of SETD3 bound to SAH and unmodified actin
9QEW 2.18 Å, Cryo-EM structure of the undecorated actin filament in the ADP-Pi state.
6MBL 2.2 Å, SETD3, a Histidine Methyltransferase, in Complex with an Actin Peptide and SAH, Second…
3D2U 2.21 Å, Structure of UL18, a Peptide-Binding Viral MHC Mimic, Bound to a Host Inhibitory Receptor

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