6WK2: SETD3 mutant

SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine. Determined by X-ray diffraction at 1.76 Å resolution. Released 17 Jun 2020.

Method: X-ray diffraction
Resolution: 1.76 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,779
Mol. weight: 141.69 kDa
Ligands: SAM
Released: 17 Jun 2020

Explore 6WK2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6WK2 contains 60 α-helices and 35 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: 30 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	21-36	16
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	139-144	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	201-225	25
α-helix	227-229	3
α-helix	233-235	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	317-319	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	378-387	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	458-493	36
α-helix	496-499	4

Chains C and Y: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	70	1	8

Chain D: 30 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	21-36	16
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	201-225	25
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	317-319	3
α-helix	320-324	5
β-strand	335-341	7	12
α-helix	349-358	10
β-strand	364-370	7	12
β-strand	376	1	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	458-493	36
α-helix	496-499	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Actin, cytoplasmic 2	C, Y	protein	23	Homo sapiens	P63261 (AlphaFold model)
Actin-histidine N-methyltransferase	A, D	protein	594	Homo sapiens	Q86TU7 (AlphaFold model)

Sequence of entity 1 (C, Y), FASTA

>6WK2_1 Actin, cytoplasmic 2 (chains C, Y)
TLKYPIEMGIVTNWDDMEKIWHH

Sequence of entity 2 (A, D), FASTA

>6WK2_2 Actin-histidine N-methyltransferase (chains A, D)
MGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVEKI
RKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEELF
LWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQTLP
SEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDSFT
YEDYRWAVSSVMTRQVQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECVAL
QDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLARA
GIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPVSW
DNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKAVK
SAAVNREYYRQQMEEKAPLPKYEESNLGLLESSVGDSRLPLVLRNLEEEAGVQDALNIRE
AISKAKATENGLVNGENSIPNGTRSENESLNQESKRAVEDAKGSSSDSTAGVKE

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	2

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

Primary citation

Characterization of SETD3 methyltransferase-mediated protein methionine methylation. Dai, S., Holt, M.V., Horton, J.R. et al. J Biol Chem (2020) 295:10901-10910. DOI 10.1074/jbc.RA120.014072 · PubMed

Other PDB entries of the same protein (UniProt P63261 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6WK1 1.89 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine
6V63 2.02 Å, SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine
6V62 2.36 Å, SETD3 double mutant (N255F/W273A) in Complex with an Actin Peptide with His73 Replaced…
7NVM 3.1 Å, Human TRiC complex in closed state with nanobody Nb18, actin and PhLP2A bound
8DNF 3.38 Å, Cryo-EM structure of nonmuscle gamma-actin
9SMX 3.67 Å, CM1-activated gTuRC in complex with nascent alpha-E254D mutant microtubules
5JLH 3.9 Å, Cryo-EM structure of a human cytoplasmic actomyosin complex at near-atomic resolution
6G2T 9.0 Å, human cardiac myosin binding protein C C1 Ig-domain bound to native cardiac thin filament
6CXI 11.0 Å, Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C…
6CXJ 11.0 Å, Cardiac thin filament decorated with C0C1 fragment of cardiac myosin binding protein C…

Browse structure collections

About this viewer

MolViewer shows 6WK2 directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.