7EA8: Human SETD2

Human SETD2 bound to a nucleosome containing oncohistone mutations. Determined by electron microscopy at 3.1 Å resolution. Released 14 Jul 2021.

Method: Electron microscopy
Resolution: 3.1 Å
Organisms: Homo sapiens, synthetic construct
Chains: 11
Atoms: 12,865
Mol. weight: 195.84 kDa
Ligands: SAM, ZN
Released: 14 Jul 2021

Explore 7EA8 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7EA8 contains 43 α-helices and 38 β-strands across 9 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: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	36	1	2
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	87-113	27
β-strand	118-119	2	8
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-93	11
β-strand	96-98	3	9

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-35	8
β-strand	42-43	2	10
α-helix	47-72	26
β-strand	77-78	2	11
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	12

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	11
α-helix	56-83	28
β-strand	88-89	2	10
α-helix	91-101	11
α-helix	105-122	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-74	11
β-strand	84	1	13
α-helix	86-113	28
β-strand	118-119	2	14
α-helix	121-131	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-40	10
β-strand	45-46	2	14
α-helix	50-75	26
β-strand	81	1	13
α-helix	83-93	11
β-strand	97-98	2	12

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	28-36	9
β-strand	42-43	2	15
α-helix	47-71	25
β-strand	77-78	2	16
α-helix	80-88	9
α-helix	93-96	4
β-strand	100-102	3	9

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	16
α-helix	56-83	28
β-strand	88-89	2	15
α-helix	91-101	11
α-helix	104-122	19

1 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETD2	L	protein	245	Homo sapiens	Q9BYW2 (AlphaFold model)
Histone H3.3	A, E	protein	101	Homo sapiens	Q6PI79 (AlphaFold model)
Histone H4	B, F	protein	78	Homo sapiens	P62799 (AlphaFold model)
Histone H2A type 1-D	C, G	protein	104	Homo sapiens	P20671 (AlphaFold model)
Histone H2B type 2-E	D, H	protein	125	Homo sapiens	P06899
601-DNA	I	DNA	122	synthetic construct
601-DNA	J	DNA	122	synthetic construct

Sequence of entity 1 (L), FASTA

>7EA8_1 Histone-lysine N-methyltransferase SETD2 (chains L)
DDFRDPQRWKECAKQGKMPCYFDLIEENVYLTERKKNKSHRDIKRMQCECTPLSKDERAQ
GEIACGEDCLNRLLMIECSSRCPNGDYCSNRRFQRKQHADVEVILTEKKGWGLRAAKDLP
SNTFVLEYCGEVLDHKEFKARVKEYARNKNIHYYFMALKNDEIIDATQKGNCSRFMNHSC
EPNCETQKWTVNGQLRVGFFTTKLVPSGSELTFDYQFQRYGKEAQKCFCGSANCRGYLGG
ENRVS

Sequence of entity 2 (A, E), FASTA

>7EA8_2 Histone H3.3 (chains A, E)
GGVMKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSAAIGAL
QEASEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGE

Sequence of entity 3 (B, F), FASTA

>7EA8_3 Histone H4 (chains B, F)
DNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTA
MDVVYALKRQGRTLYGFG

Sequence of entity 4 (C, G), FASTA

>7EA8_4 Histone H2A type 1-D (chains C, G)
AKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLTAEILELAGNAARDN
KKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLP

Sequence of entity 5 (D, H), FASTA

>7EA8_5 Histone H2B type 2-E (chains D, H)
PEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAMG
IMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTK
YTSSK

Sequence of entity 6 (I), FASTA

>7EA8_6 601-DNA (chains I)
CGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAAC
GCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGG
CA

Sequence of entity 7 (J), FASTA

>7EA8_7 601-DNA (chains J)
TGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGT
GCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCT
CG

Ligands and cofactors

ID	Name	Formula	Copies
SAM	S-adenosylmethionine	C15 H22 N6 O5 S	1
ZN	Zinc ion	Zn	3

Primary citation

Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations. Liu, Y., Zhang, Y., Xue, H. et al. Cell Discov (2021) 7:32-32. DOI 10.1038/s41421-021-00261-6 · 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
6J9J 1.78 Å, crystal structure of SESTD2 in complex with H3.3S31phK36M 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…

Browse structure collections

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