7M1X: Histone H3

Cryo-EM Structure of Nucleosome containing mouse histone variant H2A.Z. Determined by electron microscopy at 3.7 Å resolution. Released 29 Sept 2021.

Method: Electron microscopy
Resolution: 3.7 Å
Organisms: unidentified, Xenopus laevis, Mus musculus
Chains: 10
Atoms: 11,475
Mol. weight: 199.68 kDa
Released: 29 Sept 2021

Explore 7M1X in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7M1X contains 35 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: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	446-456	11
α-helix	464-478	15
β-strand	483-484	2	1
α-helix	486-513	28
β-strand	518	1	2
α-helix	521-531	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-41	11
β-strand	45	1	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-92	10
β-strand	97	1	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	819-823	5
α-helix	829-837	9
β-strand	845-846	2	4
α-helix	848-874	27
β-strand	880-881	2	5
α-helix	883-892	10
α-helix	895-899	5
β-strand	903	1	6

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1235-1245	11
β-strand	1250-1251	2	5
α-helix	1253-1280	28
β-strand	1285-1286	2	4
α-helix	1288-1298	11
α-helix	1301-1319	19

Chain E: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	645-656	12
α-helix	664-678	15
β-strand	683-684	2	7
α-helix	686-713	28
β-strand	718-719	2	8
α-helix	721-731	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	225-228	4
α-helix	231-241	11
β-strand	245-246	2	8
α-helix	250-275	26
β-strand	280-281	2	7
α-helix	283-292	10
β-strand	297	1	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1019-1022	4
α-helix	1029-1038	10
β-strand	1045-1046	2	9
α-helix	1048-1076	29
β-strand	1080-1081	2	10
α-helix	1082	1
α-helix	1083-1092	10
α-helix	1094-1099	6
β-strand	1103	1	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1445	11
β-strand	1450-1451	2	10
α-helix	1453-1480	28
β-strand	1485-1486	2	9
α-helix	1488-1498	11
α-helix	1501-1519	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA (136-mer)	I	DNA	147	unidentified
DNA (136-mer)	J	DNA	147	unidentified
Histone H3	A, E	protein	136	Xenopus laevis	P02302 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone H2A.Z	C, G	protein	128	Mus musculus	P0C0S6 (AlphaFold model)
Histone H2B 1.1	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)

Sequence of entity 1 (I), FASTA

>7M1X_1 DNA (136-MER) (chains I)
ACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCCAG

Sequence of entity 2 (J), FASTA

>7M1X_2 DNA (136-MER) (chains J)
CTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCTGT

Sequence of entity 3 (A, E), FASTA

>7M1X_3 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGEVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 4 (B, F), FASTA

>7M1X_4 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 5 (C, G), FASTA

>7M1X_5 Histone H2A.Z (chains C, G)
MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE
YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIG
KKGQQKTV

Sequence of entity 6 (D, H), FASTA

>7M1X_6 Histone H2B 1.1 (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Primary citation

Structural basis of chromatin regulation by histone variant H2A.Z. Lewis, T.S., Sokolova, V., Jung, H. et al. Nucleic Acids Res (2021) 49:11379-11391. DOI 10.1093/nar/gkab907 · 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
6PX1 3.3 Å, Set2 bound to nucleosome
8DU4 3.55 Å, Complex between RbBP5-WDR5 and an H2B-ubiquitinated nucleosome
6NZO 3.8 Å, Set2 bound to nucleosome
6PX3 4.1 Å, Set2 bound to nucleosome

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