6PX1: Set2

Set2 bound to nucleosome. Determined by electron microscopy at 3.3 Å resolution. Released 28 Aug 2019.

Method: Electron microscopy
Resolution: 3.3 Å
Organisms: Xenopus laevis, Saccharomyces cerevisiae (strain ATCC 204508 / S288c), synthetic construct
Chains: 10
Atoms: 11,937
Mol. weight: 221.05 kDa
Released: 28 Aug 2019

Explore 6PX1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6PX1 contains 37 α-helices and 20 β-strands across 8 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	26-28	3
α-helix	31-41	11
β-strand	45-46	2	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	4
α-helix	47-72	26
β-strand	77-78	2	5
α-helix	80-88	9
α-helix	91-96	6
β-strand	100-102	3	6

Chains D and H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	5
α-helix	53-80	28
β-strand	85-86	2	4
α-helix	88-98	11
α-helix	103-119	17

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
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	83-91	9
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	46-72	27
β-strand	77-78	2	10
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	3
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	136	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Ubiquitin-60S ribosomal protein L40,Histone H2A	C, G	protein	221	Saccharomyces cerevisiae (strain ATCC 204508 / S288c), Xenopus laevis	P06897 (AlphaFold model), P0CH09 (AlphaFold model)
Histone H2B 1.1	D, H	protein	123	Xenopus laevis	P02281
DNA (149-mer)	I	DNA	149	synthetic construct
DNA (149-mer)	J	DNA	149	synthetic construct

Sequence of entity 1 (A, E), FASTA

>6PX1_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVMKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6PX1_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6PX1_3 Ubiquitin-60S ribosomal protein L40,Histone H2A (chains C, G)
MDSPDLHHHHHHGTLVPRGSMQIFVKTLTGKTITLEVESSDTIDNVKSKIQDKEGIPPDQ
QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGTSSGGSGGSGGSGRSSRAGLQFPVG
RVHRLLRKGNYAERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAVR
NDEELNKLLGRVTIAQGGVLPNIQSVLLPKKTESSKSAKSK

Sequence of entity 4 (D, H), FASTA

>6PX1_4 Histone H2B 1.1 (chains D, H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 5 (I), FASTA

>6PX1_5 DNA (149-MER) (chains I)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGTGC

Sequence of entity 6 (J), FASTA

>6PX1_6 DNA (149-MER) (chains J)
GCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTT
AAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAAT
TGAGCGGCCTCGGCACCGGGATTCTCCAG

Primary citation

Nucleosome and ubiquitin position Set2 to methylate H3K36. Bilokapic, S., Halic, M. Nat Commun (2019) 10:3795-3795. DOI 10.1038/s41467-019-11726-4 · PubMed

Other PDB entries of the same protein (UniProt P02302 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1M19 2.3 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
6YN1 2.35 Å, Crystal structure of histone chaperone APLF acidic domain bound to the histone…
1M18 2.45 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1M1A 2.65 Å, Ligand binding alters the structure and dynamics of nucleosomal DNA
1AOI 2.8 Å, Complex between nucleosome core particle (H3,H4,H2A,H2B) and 146 bp long DNA fragment
8TOF 2.8 Å, Rpd3S bound to an H3K36Cme3 modified nucleosome
8ETV 3.16 Å, Class2 of the INO80-Hexasome complex
8U5H 3.23 Å, Cryo-EM structure of human DNMT3A UDR bound to H2AK119ub1-modified nucleosome
8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
7M1X 3.7 Å, Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z
6NZO 3.8 Å, Set2 bound to nucleosome
6PX3 4.1 Å, Set2 bound to nucleosome

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