7YRD: Histone methyltransferase

histone methyltransferase. Determined by electron microscopy at 3.2 Å resolution. Released 16 Aug 2023.

Method: Electron microscopy
Resolution: 3.2 Å
Organisms: Xenopus laevis, Homo sapiens
Chains: 11
Atoms: 14,275
Mol. weight: 214.81 kDa
Ligands: ZN, SAM
Released: 16 Aug 2023

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

Secondary structure: helices and β-sheets

7YRD contains 49 α-helices and 35 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
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	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97-98	2	3

Chain C: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-37	9
β-strand	45-46	2	4
α-helix	48-76	29
β-strand	80-81	2	5
α-helix	83-92	10
α-helix	94-99	6
β-strand	103	1	6
α-helix	104	1

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	32-34	3
α-helix	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	105-122	18

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	36-38	3
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
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	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	97	1	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	19-22	4
α-helix	29-36	8
β-strand	45-46	2	9
α-helix	48-75	28
β-strand	80-81	2	10
α-helix	83-92	10
α-helix	94-99	6
β-strand	103-104	2	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	10
α-helix	56-83	28
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	105-122	18

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 H3.2	A, E	protein	103	Xenopus laevis	Q71DI3 (AlphaFold model)
Histone H4	B, F	protein	102	Xenopus laevis	P62805 (AlphaFold model)
DNA (146-mer)	I, J	DNA	146	Homo sapiens
Histone H2A.Z	C, G	protein	113	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B 1.1	D, H	protein	95	Xenopus laevis	P06899 (AlphaFold model)
[histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B	K	protein	279	Homo sapiens	Q4FZB7

Sequence of entity 1 (A, E), FASTA

>7YRD_1 Histone H3.2 (chains A, E)
GEVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMAL
QEASEAYLVALFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>7YRD_2 Histone H4 (chains B, F)
SGRGKGGKGLGKGGAKRHRXVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (I, J), FASTA

>7YRD_3 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 4 (C, G), FASTA

>7YRD_4 Histone H2A.Z (chains C, G)
GKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILEYLTAEVLELA
GNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIGKKG

Sequence of entity 5 (D, H), FASTA

>7YRD_5 Histone H2B 1.1 (chains D, H)
KTRKESYAIYVYKVLKQVHPDTGISSKAMSIMNSFVNDVFERIAGEASRLAHYNKRSTIT
SREIQTAVRLLLPGELAKHAVSEGTKAVTKYTSAK

Sequence of entity 6 (K), FASTA

>7YRD_6 [histone H4]-N-methyl-L-lysine20 N-methyltransferase KMT5B (chains K)
GQSRYVPSSGMSAKELCENDDLATSLVLDPYLGFQTHKMNTRFRPIKGRQEELKEVIERF
KKDEHLEKAFKCLTSGEWARHYFLNKNKMQEKLFKEHVFIYLRMFATDSGFEILPCNRYS
SEQNGAKIVATKEWKRNDKIELLVGCIAELSEIEENMLLRHGENDFSVMYSTRKNCAQLW
LGPAAFINHDCRPNCKFVSTGRDTACVKALRDIEPGEEISCYYGDGFFGENNEFCECYTC
ERRGTGAFKSRVGLPAPAPVINSKYGLRETDKRLNRLKK

Ligands and cofactors

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

Primary citation

Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1. Huang, L., Wang, Y., Long, H. et al. Mol Cell (2023) 83:2884-2895.e7. DOI 10.1016/j.molcel.2023.07.001 · PubMed

Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide

Browse structure collections

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