2F8N: Histone H3.1

2.9 Angstrom X-ray structure of hybrid macroH2A nucleosomes. Determined by X-ray diffraction at 2.9 Å resolution. Released 23 May 2006.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Xenopus laevis, Mus musculus
Chains: 10
Atoms: 12,066
Mol. weight: 200.61 kDa
Released: 23 May 2006

Explore 2F8N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2F8N 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	441-442	2
α-helix	445-454	10
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: 3 helices, 3 β-strands

Element	Residues	Length	Sheet
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	96-98	3	3

Chain D: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1235-1245	11
β-strand	1250-1251	2	4
α-helix	1253-1280	28
β-strand	1285-1286	2	5
α-helix	1288-1298	11
α-helix	1301-1318	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	641-642	2
α-helix	645-656	12
α-helix	664-676	13
β-strand	683-684	2	6
α-helix	686-713	28
β-strand	718-719	2	7
α-helix	721-731	11

Chain F: 4 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	226-228	3
α-helix	231-240	10
β-strand	245-246	2	7
α-helix	250-275	26
β-strand	280-281	2	6
α-helix	283-292	10
β-strand	296-298	3	8

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	1017-1021	5
α-helix	1027-1037	11
β-strand	1042-1043	2	10
α-helix	1046-1072	27
β-strand	1077-1078	2	9
α-helix	1080-1088	9
α-helix	1091-1096	6
β-strand	1100-1102	3	3
α-helix	1113-1115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1435-1443	9
β-strand	1450-1451	2	9
α-helix	1453-1480	28
β-strand	1485-1486	2	10
α-helix	1488-1498	11
α-helix	1501-1519	19

Chain K: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-21	5
α-helix	27-36	10
β-strand	42-43	2	5
α-helix	47-72	26
β-strand	77-78	2	4
α-helix	80-89	10
α-helix	91-96	6
β-strand	100-102	3	8
α-helix	113-115	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
alpha-satellite DNA (146 bp)	I, J	DNA	146	Homo sapiens
Histone H3.1	A, E	protein	136	Xenopus laevis	P84233 (AlphaFold model)
Histone H4	B, F	protein	103	Xenopus laevis	P62799 (AlphaFold model)
Histone 3, H2ba	D	protein	126	Mus musculus	Q9D2U9 (AlphaFold model)
Histone H2B.1	H	protein	123	Xenopus laevis	P02281 (AlphaFold model)
Core histone macro-H2A.1	G	protein	120	Homo sapiens	O75367
Histone H2A type 1	K	protein	149	Mus musculus	Q8CGP6

Sequence of entity 1 (I, J), FASTA

>2F8N_1 alpha-satellite DNA (146 bp) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCGGAATTCCGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Sequence of entity 2 (A, E), FASTA

>2F8N_2 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA

Sequence of entity 3 (B, F), FASTA

>2F8N_3 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 4 (D), FASTA

>2F8N_4 Histone 3, H2ba (chains D)
MPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTKAVT
KYTSSK

Sequence of entity 5 (H), FASTA

>2F8N_5 Histone H2B.1 (chains H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK

Sequence of entity 6 (G), FASTA

>2F8N_6 Core histone macro-H2A.1 (chains G)
MSSRGGKKKSTKTSRSAKAGVIFPVGRMLRYIKKGHPKYRIGVGAPVYMAAVLEYLTAEI
LELAVNAARDNKKGRVTPRHILLAVANDEELNQLLKGVTIASGGVLPNIHPELLAKKRGS

Sequence of entity 7 (K), FASTA

>2F8N_7 Histone H2A type 1 (chains K)
MGSSHHHHHHSSGLVPRGSMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYS
ERVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRV
TIAQGGVLPNIQAVLLPKKTESHHKAKGK

Primary citation

Nucleosomes containing the histone domain of macroH2A: In vitro possibilities. Chakravarthy, S., Luger, K. To be published.

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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