5HQ2: Histone H3.2

Structural model of Set8 histone H4 Lys20 methyltransferase bound to nucleosome core particle. Determined by X-ray diffraction at 4.5 Å resolution. Released 23 Mar 2016.

Method: X-ray diffraction
Resolution: 4.5 Å
Organisms: Xenopus laevis, synthetic construct, Saccharomyces cerevisiae (strain ATCC 204508 / S288c)
Chains: 8
Atoms: 7,738
Mol. weight: 222.17 kDa
Released: 23 Mar 2016

Explore 5HQ2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5HQ2 contains 34 α-helices and 57 β-strands across 6 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	45-54	10
α-helix	64-78	15
β-strand	83-84	2	1
α-helix	86-112	27
β-strand	119	1	2
α-helix	121-131	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	31-39	9
β-strand	46	1	2
α-helix	50-74	25
β-strand	80-81	2	1
α-helix	82	1
α-helix	83-93	11
β-strand	97-98	2	3

Chain G: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	29-37	9
β-strand	43	1	4
α-helix	46-73	28
α-helix	78-79	2
α-helix	80-87	8
α-helix	91-96	6
β-strand	101-102	2	3

Chain H: 5 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	35-45	11
α-helix	55-58	4
α-helix	60-79	20
β-strand	86	1	4
α-helix	88-98	11
α-helix	101-119	19

Chain K: 8 helices, 33 β-strands

Element	Residues	Length	Sheet
α-helix	34-36	3
α-helix	46	1
β-strand	47-48	2	5
α-helix	81-84	4
β-strand	88-90	3	6
β-strand	96-99	4	6
β-strand	106-108	3	6
α-helix	146-148	3
β-strand	151-152	2	6
α-helix	153-154	2
β-strand	167	1	7
β-strand	171	1	8
β-strand	176-177	2	9
β-strand	178	1	8
β-strand	180	1	9
β-strand	181	1	7
β-strand	186-190	5	9
β-strand	192-193	2	10
α-helix	194	1
β-strand	199-200	2	10
β-strand	209-215	7	9
α-helix	222-223	2
β-strand	236	1	11
β-strand	242	1	11
β-strand	274-277	4	12
β-strand	286-288	3	12
β-strand	294	1	12
β-strand	330-335	6	13
β-strand	339-344	6	13
β-strand	349-354	6	13
β-strand	372-373	2	13
β-strand	379-382	4	13
β-strand	394-397	4	14
β-strand	403-405	3	15
β-strand	406-408	3	14
β-strand	413-414	2	16
β-strand	415-417	3	15
β-strand	438-439	2	16
β-strand	448-449	2	5
β-strand	462-464	3	5
α-helix	468-474	7

Chain M: 7 helices, 16 β-strands

Element	Residues	Length	Sheet
α-helix	195-212	18
β-strand	219-223	5	17
β-strand	227-231	5	17
β-strand	236	1	18
β-strand	241-244	4	19
β-strand	248	1	20
α-helix	258-262	5
β-strand	276	1	21
β-strand	281	1	21
β-strand	285	1	20
α-helix	294-296	3
α-helix	297	1
β-strand	298-299	2	22
β-strand	306-309	4	19
β-strand	312	1	23
β-strand	315	1	23
β-strand	318-321	4	19
β-strand	326	1	18
α-helix	327	1
β-strand	331-332	2	17
β-strand	333-334	2	22
α-helix	341-346	6
α-helix	348-350	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.2	A	protein	135	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B	protein	102	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A	G	protein	129	Xenopus laevis	P06897 (AlphaFold model)
Histone H2B 1.1	H	protein	122	Xenopus laevis	P02281 (AlphaFold model)
DNA (149-mer)	I	DNA	149	synthetic construct
DNA (149-mer)	J	DNA	149	synthetic construct
Guanine nucleotide exchange factor SRM1	K	protein	483	Saccharomyces cerevisiae (strain ATCC 204508 / S288c)	P21827
N-lysine methyltransferase SETD8	M	protein	202	Homo sapiens	Q9NQR1

Sequence of entity 1 (A), FASTA

>5HQ2_1 Histone H3.2 (chains A)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 2 (B), FASTA

>5HQ2_2 Histone H4 (chains B)
SGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLKV
FLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (G), FASTA

>5HQ2_3 Histone H2A (chains G)
SGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKKT
ESSKSAKSK

Sequence of entity 4 (H), FASTA

>5HQ2_4 Histone H2B 1.1 (chains H)
AKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIMN
SFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYTS
AK

Sequence of entity 5 (I), FASTA

>5HQ2_5 DNA (149-MER) (chains I)
ATCGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTA
AACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCC
AGGCACGTGTCAGATATATACATCCTGAT

Sequence of entity 6 (J), FASTA

>5HQ2_6 DNA (149-MER) (chains J)
ATCAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTA
AAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATT
GAGCGGCCTCGGCACCGGGATTCTCCGAT

Sequence of entity 7 (K), FASTA

>5HQ2_7 Guanine nucleotide exchange factor SRM1 (chains K)
GSVKRTVATNGDASGAHRAKKMSKTHASHIINAQEDYKHMYLSVQPLDIFCWGTGSMCEL
GLGPLAKNKEVKRPRLNPFLPRDEAKIISFAVGGMHTLALDEESNVWSWGCNDVGALGRD
TSNAKEQLKDMDADDSSDDEDGDLNELESTPAKIPRESFPPLAEGHKVVQLAATDNMSCA
LFSNGEVYAWGTFRCNEGILGFYQDKIKIQKTPWKVPTFSKYNIVQLAPGKDHILFLDEE
GMVFAWGNGQQNQLGRKVMERFRLKTLDPRPFGLRHVKYIASGENHCFALTKDNKLVSWG
LNQFGQCGVSEDVEDGALVTKPKRLALPDNVVIRSIAAGEHHSLILSQDGDLYSCGRLDM
FEVGIPKDNLPEYTYKDVHGKARAVPLPTKLNNVPKFKSVAAGSHHSVAVAQNGIAYSWG
FGETYAVGLGPFEDDTEVPTRIKNTATQDHNIILVGCGGQFSVSGGVKLSDEDAEKRADE
MDD

Sequence of entity 8 (M), FASTA

>5HQ2_8 N-lysine methyltransferase SETD8 (chains M)
GSAKQALKKPIKGKQAPRKKAQGKTQQNRKLTDFYPVRRSSRKSKAELQSEERKRIDELI
ESGKEEGMKIDLIDGKGRGVIATKQFSRGDFVVEYHGDLIEITDAKKREALYAQDPSTGC
YMYYFQYLSKTYCVDATRETNRLGRLINHSKCGNCQTKLHDIDGVPHLILIASRDIAAGE
ELLYDYGDRSKASIEAFPWLKH

Primary citation

Multivalent Interactions by the Set8 Histone Methyltransferase With Its Nucleosome Substrate. Girish, T.S., McGinty, R.K., Tan, S. J Mol Biol (2016) 428:1531-1543. DOI 10.1016/j.jmb.2016.02.025 · PubMed

Other PDB entries of the same protein (UniProt P84233 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2HUE 1.7 Å, Structure of the H3-H4 chaperone Asf1 bound to histones H3 and H4
3GV6 1.76 Å, Crystal Structure of human chromobox homolog 6 (CBX6) with H3K9 peptide
1KX5 1.94 Å, X-Ray Structure of the Nucleosome Core Particle, NCP147, at 1.9 A Resolution
1KX3 2.0 Å, X-Ray Structure of the Nucleosome Core Particle, NCP146, at 2.0 A Resolution
4QEO 2.0 Å, crystal structure of KRYPTONITE in complex with mCHH DNA, H3(1-15) peptide and SAH
1S32 2.05 Å, Molecular Recognition of the Nucleosomal 'Supergroove'
3UTA 2.07 Å, Crystal Structure of Nucleosome Core Particle Assembled with an Alpha-Satellite Sequence…
3C1B 2.2 Å, The effect of H3 K79 dimethylation and H4 K20 trimethylation on nucleosome and chromatin…
3UT9 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with a Palindromic Widom '601'…
3UTB 2.2 Å, Crystal Structure of Nucleosome Core Particle Assembled with the 146b Alpha-Satellite…
6WZ5 2.2 Å, Bridging of double-strand DNA break activates PARP2/HPF1 to modify chromatin
8RUQ 2.29 Å, Borealin N-terminus in complex with H3.T3p-nucleosome

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