6J9J: SESTD2

crystal structure of SESTD2 in complex with H3.3S31phK36M peptide. Determined by X-ray diffraction at 1.78 Å resolution. Released 26 Feb 2020.

Method: X-ray diffraction
Resolution: 1.78 Å
Organism: Homo sapiens
Chains: 2
Atoms: 2,396
Mol. weight: 32.15 kDa
Ligands: SCN, SAH, ZN
Released: 26 Feb 2020

Explore 6J9J in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6J9J contains 15 α-helices and 22 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: 15 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	1448-1450	3	1
α-helix	1451-1455	5
α-helix	1457-1465	9
α-helix	1470-1472	3
β-strand	1474-1475	2	2
β-strand	1480-1481	2	3
α-helix	1501-1505	5
α-helix	1506-1510	5
α-helix	1513-1514	2
α-helix	1521-1524	4
β-strand	1527	1	4
α-helix	1536-1538	3
β-strand	1552-1556	5	1
β-strand	1562-1566	5	1
β-strand	1570	1	5
β-strand	1575-1578	4	4
β-strand	1582-1584	3	3
α-helix	1586-1598	13
β-strand	1606-1610	5	3
β-strand	1613-1616	4	3
β-strand	1620-1621	2	2
α-helix	1623-1626	4
α-helix	1627	1
β-strand	1628-1629	2	4
β-strand	1635-1642	8	4
β-strand	1645-1652	8	4
β-strand	1656	1	5
α-helix	1660	1
β-strand	1661-1662	2	1
β-strand	1663-1664	2	4
β-strand	1669-1670	2	3
α-helix	1675	1
β-strand	1676-1677	2	6
α-helix	1678	1
β-strand	1688-1689	2	6
α-helix	1697-1700	4

Chain B: 0 helices, 1 β-strand

Element	Residues	Length	Sheet
β-strand	34-36	3	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD2	A	protein	257	Homo sapiens	Q9BYW2 (AlphaFold model)
H3.3S31phK36M(29-42)	B	protein	14	Homo sapiens	P84243 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>6J9J_1 Histone-lysine N-methyltransferase SETD2 (chains A)
PSCVMDDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERAKNKSHRDIKRMQCECTPLSK
DERAQGEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRA
AKDLPSNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRF
MNHSCEPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCR
GYLGGENRVSIRAAGGK

Sequence of entity 2 (B), FASTA

>6J9J_2 H3.3S31phK36M(29-42) (chains B)
APSTGGVMKPHRYR

Ligands and cofactors

ID	Name	Formula	Copies
SCN	Thiocyanate ion	C N S	4
SAH	S-adenosyl-L-homocysteine	C14 H20 N6 O5 S	1
ZN	Zinc ion	Zn	3

Primary citation

Histone H3.3 phosphorylation amplifies stimulation-induced transcription. Armache, A., Yang, S., Martinez de Paz, A. et al. Nature (2020) 583:852-857. DOI 10.1038/s41586-020-2533-0 · PubMed

Other PDB entries of the same protein (UniProt Q9BYW2 (AlphaFold model), which also has an AlphaFold model), best resolution first:

5JLB 1.5 Å, Crystal structure of SETD2 bound to histone H3.3 K36I peptide
5LT7 1.51 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LT8 1.57 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVS 1.6 Å, Crystal structure of hnRNP LL RRM2 in complex with SETD2
5LSY 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
5LSZ 1.62 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
9G4A 1.65 Å, Structure of human SETD2 T1663M mutant in complex with SAM and H3K36M peptide
5LSS 1.79 Å, Structure of the Epigenetic Oncogene MMSET and inhibition by N-Alkyl Sinefungin…
7EVR 1.8 Å, Crystal structure of hnRNP L RRM2 in complex with SETD2
7LZD 1.8 Å, Crystal Structure of SETD2 bound to Compound 35
8Q5P 1.81 Å, Structure of the lysine methyltransferase SETD2 in complex with a peptide derived from…
9HGG 1.9 Å, SETD2 peptide bound to SPOP MATH domain

Browse structure collections

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