1F66: Histone H3

2.6 a crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Determined by X-ray diffraction at 2.6 Å resolution. Released 27 Nov 2000.

Method: X-ray diffraction
Resolution: 2.6 Å
Organisms: Xenopus laevis, Mus musculus, Homo sapiens
Chains: 10
Atoms: 12,397
Mol. weight: 199.86 kDa
Ligands: MN
Released: 27 Nov 2000

Explore 1F66 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

1F66 contains 39 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	819-823	5
α-helix	829-838	10
β-strand	845-846	2	4
α-helix	850-874	25
β-strand	880-881	2	5
α-helix	883-892	10
α-helix	894-899	6
β-strand	903-904	2	6
α-helix	915-917	3

Chain D: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1230-1232	3
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	645-655	11
α-helix	664-676	13
β-strand	683-684	2	7
α-helix	686-713	28
β-strand	718-719	2	8
α-helix	721-731	11

Chain F: 5 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	282	1
α-helix	283-292	10
β-strand	297-298	2	6

Chain G: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1019-1023	5
α-helix	1029-1037	9
β-strand	1045-1046	2	9
α-helix	1050-1074	25
β-strand	1080-1081	2	10
α-helix	1083-1092	10
α-helix	1094-1099	6
β-strand	1103-1104	2	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
Palindromic 146 base pair DNA fragment	I, J	DNA	146
Histone H3	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Mus musculus	P62806 (AlphaFold model)
Histone H2A.Z	C, G	protein	128	Homo sapiens	P0C0S5 (AlphaFold model)
Histone H2B	D, H	protein	126	Xenopus laevis	P02281 (AlphaFold model)

Sequence of entity 1 (I, J), FASTA

>1F66_1 PALINDROMIC 146 BASE PAIR DNA FRAGMENT (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>1F66_2 HISTONE H3 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGEVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>1F66_3 HISTONE H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (C, G), FASTA

>1F66_4 HISTONE H2A.Z (chains C, G)
MAGGKAGKDSGKAKTKAVSRSQRAGLQFPVGRIHRHLKSRTTSHGRVGATAAVYSAAILE
YLTAEVLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGGVIPHIHKSLIG
KKGQQKTV

Sequence of entity 5 (D, H), FASTA

>1F66_5 HISTONE H2B (chains D, H)
MPEPAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAM
SIMNSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	15

Primary citation

Crystal structure of a nucleosome core particle containing the variant histone H2A.Z. Suto, R.K., Clarkson, M.J., Tremethick, D.J. et al. Nat Struct Biol (2000) 7:1121-1124. DOI 10.1038/81971 · 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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