6DZT: Nucleosome

Cryo-EM structure of nucleosome in complex with a single chain antibody fragment. Determined by electron microscopy at 2.99 Å resolution. Released 22 May 2019.

Method: Electron microscopy
Resolution: 2.99 Å
Organisms: Drosophila melanogaster, Escherichia coli, Mus musculus
Chains: 12
Atoms: 15,621
Mol. weight: 257.15 kDa
Released: 22 May 2019

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

Secondary structure: helices and β-sheets

6DZT contains 44 α-helices and 74 β-strands across 10 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: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-74	11
α-helix	75-77	3
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chains B and 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	2
α-helix	50-75	26
β-strand	80-81	2	1
α-helix	83-91	9
β-strand	96-98	3	3

Chains C and G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
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
α-helix	113-115	3

Chain D: 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	103-118	16

Chain E: 6 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-54	10
α-helix	64-74	11
α-helix	75-77	3
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	35-45	11
β-strand	50-51	2	10
α-helix	53-80	28
β-strand	85-86	2	9
α-helix	88-98	11
α-helix	103-119	17

Chain M: 1 helix, 26 β-strands

Element	Residues	Length	Sheet
β-strand	25-28	4	11
β-strand	32-34	3	12
β-strand	40-43	4	13
β-strand	44-47	4	11
α-helix	51-53	3
β-strand	54-62	9	12
β-strand	66-74	9	12
β-strand	79-82	4	12
β-strand	87	1	13
β-strand	90-95	6	13
β-strand	100-105	6	13
β-strand	114-122	9	12
β-strand	129-132	4	12
β-strand	136-140	5	12
β-strand	163-164	2	14
β-strand	168-171	4	15
β-strand	177-180	4	16
β-strand	181-182	2	14
β-strand	187	1	17
β-strand	191-196	6	15
β-strand	203-207	5	15
β-strand	211-212	2	15
β-strand	220-224	5	16
β-strand	226	1	17
β-strand	229-233	5	16
β-strand	243-248	6	15
β-strand	261-264	4	15

Chain N: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	25-26	2	18
β-strand	32-33	2	19
β-strand	40-43	4	20
β-strand	46-47	2	18
α-helix	51-53	3
β-strand	54-62	9	21
β-strand	66-74	9	21
β-strand	79-82	4	21
α-helix	84-86	3
β-strand	87	1	20
β-strand	90-95	6	20
β-strand	100-105	6	20
β-strand	115-122	8	21
β-strand	129-132	4	21
β-strand	136-137	2	21
β-strand	138-139	2	19
β-strand	162	1	22
β-strand	163-164	2	23
β-strand	168-171	4	24
β-strand	177-180	4	25
β-strand	181-182	2	23
β-strand	191-196	6	24
β-strand	203-207	5	24
β-strand	211-212	2	24
β-strand	221-225	5	25
β-strand	228-233	6	25
α-helix	238-240	3
β-strand	243-248	6	24
β-strand	255-256	2	24
β-strand	257	1	22
β-strand	261-264	4	24

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3	A, E	protein	136	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	104	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G	protein	124	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	124	Drosophila melanogaster	P02283 (AlphaFold model)
DNA (147-mer)	I	DNA	147	Escherichia coli
DNA (147-mer)	J	DNA	147	Escherichia coli
scFv	M, N	protein	265	Mus musculus

Sequence of entity 1 (A, E), FASTA

>6DZT_1 Histone H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>6DZT_2 Histone H4 (chains B, F)
MITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVL
KVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>6DZT_3 Histone H2A (chains C, G)
MSGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAA
EVLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKT
EKKA

Sequence of entity 4 (D, H), FASTA

>6DZT_4 Histone H2B (chains D, H)
MIPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSI
MNSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKY
TSSK

Sequence of entity 5 (I), FASTA

>6DZT_5 DNA (147-MER) (chains I)
ATCGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTTAA
AACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAATTG
AGCGGCCTCGGCACCGGGATTCTCGAT

Sequence of entity 6 (J), FASTA

>6DZT_6 DNA (147-MER) (chains J)
ATCGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAA
ACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCA
GGCACGTGTCAGATATATACATCCGAT

Sequence of entity 7 (M, N), FASTA

>6DZT_7 scFv (chains M, N)
MKSSHHHHHHENLYFQSNAMEVQLQQSGPELVEPGTSVKMPCKASGYTFTSYTIQWVKQT
PRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSEDSAVYYCARKS
SRLRSTLDYWGQGTSVTVSSGGGGSGGGGSGGGGSMDIKMTQSPSSMHASLGERVTITCK
ASQDIRSYLSWYQQKPWKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTA
TYYCLQHGESPYTFGSGTKLEIKRA

Primary citation

Atomic resolution cryo-EM structure of a native-like CENP-A nucleosome aided by an antibody fragment. Zhou, B.R., Yadav, K.N.S., Borgnia, M. et al. Nat Commun (2019) 10:2301-2301. DOI 10.1038/s41467-019-10247-4 · PubMed

Other PDB entries of the same protein (UniProt P02299 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6AT0 1.28 Å, Chromodomain HP1 with a p-nitro-L-phenylalanine mutation at position 24 bound to histone…
6MHA 1.5 Å, dHP1 Chromodomain Y24W variant bound to histone H3 peptide containing trimethyllysine
6ASZ 1.52 Å, Chromodomain HP1 with Y24F mutation bound to histone H3 peptide containing trimethyl…
7VRF 1.7 Å, Crystal structure of Oxpecker chromodomain in complex with H3K9me3
1KNA 2.1 Å, Chromo domain of HP1 complexed with histone H3 tail containing dimethyllysine 9.
9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
2NQB 2.3 Å, Drosophila Nucleosome Structure
9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
1KNE 2.4 Å, Chromo domain of HP1 complexed with histone H3 tail containing trimethyllysine 9
2PYO 2.43 Å, Drosophila nucleosome core
8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
4QUF 2.5 Å, crystal structure of chromodomain of Rhino with H3K9me3

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