3A6N: Histone H3.1t

The nucleosome containing a testis-specific histone variant, human H3T. Determined by X-ray diffraction at 2.7 Å resolution. Released 26 May 2010.

Method: X-ray diffraction
Resolution: 2.7 Å
Organism: Homo sapiens
Chains: 10
Atoms: 12,062
Mol. weight: 203.02 kDa
Ligands: MN
Released: 26 May 2010

Explore 3A6N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3A6N 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	41-42	2
α-helix	45-56	12
α-helix	64-75	12
β-strand	83-84	2	1
α-helix	86-113	28
β-strand	118-119	2	2
α-helix	121-130	10

Chain B: 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	83-92	10
β-strand	97-98	2	3

Chain C: 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	46-72	27
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	38-48	11
β-strand	53-54	2	5
α-helix	56-83	28
β-strand	88-89	2	4
α-helix	91-101	11
α-helix	104-121	18

Chain E: 5 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	41-42	2
α-helix	45-56	12
α-helix	64-78	15
β-strand	83-84	2	7
α-helix	86-113	28
β-strand	118-119	2	8
α-helix	121-131	11

Chain F: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	20-22	3
α-helix	25-28	4
α-helix	31-40	10
β-strand	45-46	2	8
α-helix	50-75	26
β-strand	80-81	2	7
α-helix	83-92	10
β-strand	96-98	3	6

Chain G: 6 helices, 3 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	27-35	9
β-strand	42-43	2	9
α-helix	47-71	25
β-strand	77-78	2	10
α-helix	80-88	9
α-helix	91-96	6
β-strand	101-102	2	3
α-helix	113-115	3

Chain H: 4 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	38-48	11
β-strand	53-54	2	10
α-helix	56-83	28
β-strand	88-89	2	9
α-helix	91-101	11
α-helix	104-122	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone H3.1t	A, E	protein	139	Homo sapiens	Q16695 (AlphaFold model)
Histone H4	B, F	protein	106	Homo sapiens	P62805 (AlphaFold model)
Histone H2A type 1-B/E	C, G	protein	133	Homo sapiens	P04908 (AlphaFold model)
Histone H2B type 1-J	D, H	protein	129	Homo sapiens	P06899 (AlphaFold model)
146-mer DNA	I, J	DNA	146

Sequence of entity 1 (A, E), FASTA

>3A6N_1 Histone H3.1t (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYRPGTVALREIRRYQK
STELLIRKLPFQRLMREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCVIHAKR
VTIMPKDIQLARRIRGERA

Sequence of entity 2 (B, F), FASTA

>3A6N_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG

Sequence of entity 3 (C, G), FASTA

>3A6N_3 Histone H2A type 1-B/E (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK

Sequence of entity 4 (D, H), FASTA

>3A6N_4 Histone H2B type 1-J (chains D, H)
GSHMPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTK
AVTKYTSAK

Sequence of entity 5 (I, J), FASTA

>3A6N_5 146-MER DNA (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT

Ligands and cofactors

ID	Name	Formula	Copies
MN	Manganese (II) ion	Mn	8

Water and common crystallization additives (CL) are not listed.

Primary citation

Structural basis of instability of the nucleosome containing a testis-specific histone variant, human H3T. Tachiwana, H., Kagawa, W., Osakabe, A. et al. Proc Natl Acad Sci U S A (2010) 107:10454-10459. DOI 10.1073/pnas.1003064107 · PubMed

Other PDB entries of the same protein (UniProt Q16695 (AlphaFold model), which also has an AlphaFold model), best resolution first:

21EE 1.34 Å, Crystal structure of human PHF20L1(1-80) in complex with H3K36me
3MO8 1.69 Å, PWWP Domain of Human Bromodomain and PHD finger-containing protein 1 In Complex with…
6WAU 1.75 Å, Complex structure of PHF19
6WAT 1.8 Å, complex structure of PHF1
4V2W 1.81 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (16-35)
3T6R 1.95 Å, Structure of UHRF1 in complex with unmodified H3 N-terminal tail
4V2V 2.0 Å, JMJD2A complexed with ni(ii), nog and histone H3K27me3 peptide (25-29) ARK(me3)SA
2YBP 2.02 Å, JMJD2A complexed with R-2-hydroxyglutarate and histone H3K36me3 peptide (30-41)
6OIE 2.08 Å, The double PHD finger (DPF) of MORF in complex with histone H3K14cr
2YBS 2.32 Å, JMJD2A complexed with S-2-hydroxyglutarate and histone H3K36me3 peptide (30-41)
8Z50 2.8 Å, Crystal structure of the ASF1-H3T-H4 complex
2V1D 3.1 Å, Structural basis of LSD1-CoREST selectivity in histone H3 recognition

Browse structure collections

About this viewer

MolViewer shows 3A6N 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.