6V63: SETD3 WT

SETD3 WT in Complex with an Actin Peptide with His73 Replaced with Glutamine. Determined by X-ray diffraction at 2.02 Å resolution. Released 22 Jan 2020.

Method: X-ray diffraction
Resolution: 2.02 Å
Organism: Homo sapiens
Chains: 4
Atoms: 8,985
Mol. weight: 143.94 kDa
Ligands: SAH
Released: 22 Jan 2020

Explore 6V63 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6V63 contains 59 α-helices and 33 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: 29 helices, 15 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	317-322	6
β-strand	335-341	7	6
α-helix	349-358	10
β-strand	364-370	7	6
α-helix	378-387	10
α-helix	391-396	6
α-helix	403-408	6
α-helix	419-437	19
α-helix	444-453	10
α-helix	458-493	36
α-helix	496-499	4

Chain B: 30 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	8
β-strand	104-109	6	8
β-strand	113	1	9
β-strand	118-123	6	7
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	7
β-strand	293-297	5	7
β-strand	302	1	9
β-strand	307-308	2	8
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
α-helix	458-493	36
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, cytoplasmic 1	Y, Z	protein	23	Homo sapiens	P63261 (AlphaFold model)
Actin-histidine N-methyltransferase	A, B	protein	596	Homo sapiens	Q86TU7 (AlphaFold model)

Sequence of entity 1 (Y, Z), FASTA

>6V63_1 Actin, cytoplasmic 1 (chains Y, Z)
TLKYPIEQGIVTNWDDMEKIWHH

Sequence of entity 2 (A, B), FASTA

>6V63_2 Actin-histidine N-methyltransferase (chains A, B)
GSMGKKSRVKTQKSGTGATATVSPKEILNLTSELLQKCSSPAPGPGKEWEEYVQIRTLVE
KIRKKQKGLSVTFDGKREDYFPDLMKWASENGASVEGFEMVNFKEEGFGLRATRDIKAEE
LFLWVPRKLLMTVESAKNSVLGPLYSQDRILQAMGNIALAFHLLCERASPNSFWQPYIQT
LPSEYDTPLYFEEDEVRYLQSTQAIHDVFSQYKNTARQYAYFYKVIQTHPHANKLPLKDS
FTYEDYRWAVSSVMTRQNQIPTEDGSRVTLALIPLWDMCNHTNGLITTGYNLEDDRCECV
ALQDFRAGEQIYIFYGTRSNAEFVIHSGFFFDNNSHDRVKIKLGVSKSDRLYAMKAEVLA
RAGIPTSSVFALHFTEPPISAQLLAFLRVFCMTEEELKEHLLGDSAIDRIFTLGNSEFPV
SWDNEVKLWTFLEDRASLLLKTYKTTIEEDKSVLKNHDLSVRAKMAIKLRLGEKEILEKA
VKSAAVNREYYRQQMEEKAPLPKYEESNLGLLESSVGDSRLPLVLRNLEEEAGVQDALNI
REAISKAKATENGLVNGENSIPNGTRSENESLNQESKRAVEDAKGSSSDSTAGVKE

Ligands and cofactors

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

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

Primary citation

An engineered variant of SETD3 methyltransferase alters target specificity from histidine to lysine methylation. Dai, S., Horton, J.R., Wilkinson, A.W. et al. J Biol Chem (2020) 295:2582-2589. DOI 10.1074/jbc.RA119.012319 · PubMed

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

6WK2 1.76 Å, SETD3 mutant (N255V) in Complex with an Actin Peptide with His73 Replaced with Methionine
6WK1 1.89 Å, SETD3 in Complex with an Actin Peptide with His73 Replaced with Methionine
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…

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