2NQB: Drosophila Nucleosome Structure

Drosophila Nucleosome Structure. Determined by X-ray diffraction at 2.3 Å resolution. Released 11 Sept 2007.

Method: X-ray diffraction
Resolution: 2.3 Å
Organisms: Homo sapiens, Drosophila melanogaster
Chains: 10
Atoms: 12,294
Mol. weight: 197.35 kDa
Released: 11 Sept 2007

Explore 2NQB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2NQB contains 38 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	441-442	2
α-helix	445-456	12
α-helix	464-476	13
β-strand	483-484	2	1
α-helix	486-513	28
β-strand	518-519	2	2
α-helix	521-531	11

Chain B: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	25-28	4
α-helix	31-40	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	817-821	5
α-helix	827-836	10
β-strand	842-843	2	4
α-helix	846-872	27
β-strand	877-878	2	5
α-helix	880-888	9
α-helix	891-896	6
β-strand	900-902	3	6
α-helix	913-915	3

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	1301-1320	20

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	641-642	2
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	231-240	10
β-strand	245-246	2	8
α-helix	250-275	26
β-strand	280-281	2	7
α-helix	283-292	10
β-strand	296-298	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1017-1021	5
α-helix	1027-1036	10
β-strand	1042-1043	2	9
α-helix	1046-1072	27
β-strand	1077-1078	2	10
α-helix	1080-1088	9
α-helix	1091-1096	6
β-strand	1101-1102	2	3
α-helix	1113-1115	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
alpha-satellite DNA	I, J	DNA	146	Homo sapiens
Histone H3	A, E	protein	135	Drosophila melanogaster	P02299 (AlphaFold model)
Histone H4	B, F	protein	103	Drosophila melanogaster	P84040 (AlphaFold model)
Histone H2A	C, G	protein	123	Drosophila melanogaster	P84051 (AlphaFold model)
Histone H2B	D, H	protein	123	Drosophila melanogaster	P02283 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>2NQB_1 alpha-satellite DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>2NQB_2 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>2NQB_3 Histone H4 (chains B, F)
ITGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>2NQB_4 Histone H2A (chains C, G)
SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE
KKA

Sequence of entity 5 (D, H), FASTA

>2NQB_5 Histone H2B (chains D, H)
IPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYTVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK

Primary citation

Comparative analysis of nucleosome structures from different species. Chakravarthy, S., Luger, K. To be published.

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
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
2YBA 2.55 Å, Crystal structure of Nurf55 in complex with histone H3

Browse structure collections

About this viewer

MolViewer shows 2NQB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.