5B1L: The mouse nucleosome structure containing H3t
The mouse nucleosome structure containing H3t. Determined by X-ray diffraction at 2.35 Å resolution. Released 15 Feb 2017.
- Method
- X-ray diffraction
- Resolution
- 2.35 Å
- Organisms
- Mus musculus, Homo sapiens
- Chains
- 10
- Atoms
- 12,164
- Mol. weight
- 203.32 kDa
- Ligands
- MN
- Released
- 15 Feb 2017
Explore 5B1L in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5B1L 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.
Chains A and 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 | 1 |
| α-helix | 86-113 | 28 | |
| β-strand | 118-119 | 2 | 2 |
| α-helix | 121-131 | 11 | |
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: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 12-14 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| 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 | 101-102 | 2 | 6 |
| α-helix | 113-115 | 3 | |
Chains D and H: 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 | 104-123 | 20 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| 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 | 97-98 | 2 | 6 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 9 |
| α-helix | 46-72 | 27 | |
| 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 | |
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3t | A, E | protein | 139 | Mus musculus | P68433 (AlphaFold model) |
| Histone H4 | B, F | protein | 106 | Mus musculus | P62806 (AlphaFold model) |
| Histone H2A type 1 | C, G | protein | 133 | Mus musculus | C0HKE1 (AlphaFold model) |
| Histone H2B type 3-A | D, H | protein | 129 | Mus musculus | Q9D2U9 (AlphaFold model) |
| DNA (146-mer) | I, J | DNA | 146 | Homo sapiens | |
Sequence of entity 1 (A, E), FASTA
>5B1L_1 Histone H3t (chains A, E)
GSHMARTKQTARKSTGGKAPRKQLATKVARKSAPATGGVKKPHRYHPGTVALREIRRYQK
STELLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACESYLVGLFEDTNLCAIHAKR
VTIMPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>5B1L_2 Histone H4 (chains B, F)
GSHMSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRG
VLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>5B1L_3 Histone H2A type 1 (chains C, G)
GSHMSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLE
YLTAEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLL
PKKTESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>5B1L_4 Histone H2B type 3-A (chains D, H)
GSHMPEPSRSTPAPKKGSKKAITKAQKKDGKKRKRGRKESYSIYVYKVLKQVHPDTGISS
KAMGIMNSFVNDIFERIASEASRLAHYNKRSTITSREVQTAVRLLLPGELAKHAVSEGTK
AVTKYTSSK
Sequence of entity 5 (I, J), FASTA
>5B1L_5 DNA (146-MER) (chains I, J)
ATCAATATCCACCTGCAGATTCTACCAAAAGTGTATTTGGAAACTGCTCCATCAAAAGGC
ATGTTCAGCTGAATTCAGCTGAACATGCCTTTTGATGGAGCAGTTTCCAAATACACTTTT
GGTAGAATCTGCAGGTGGATATTGAT
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| MN | Manganese (II) ion | Mn | 13 |
Water and common crystallization additives (CL) are not listed.
Primary citation
Testis-Specific Histone Variant H3t Gene Is Essential for Entry into Spermatogenesis. Ueda, J., Harada, A., Urahama, T. et al. Cell Rep (2017) 18:593-600. DOI 10.1016/j.celrep.2016.12.065 · PubMed
Other PDB entries of the same protein (UniProt P68433 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 7QPH 1.9 Å, Crystal structure of mouse CARM1 in complex with histone H3_22-31 K27 acetylated
- 7QRD 2.0 Å, Crystal structure of mouse CARM1 in complex with histone H3_10-25
- 2WP1 2.1 Å, Structure of Brdt bromodomain 2 bound to an acetylated histone H3 peptide
- 2W5Z 2.2 Å, Ternary Complex of the Mixed Lineage Leukaemia (MLL1) SET Domain with the cofactor…
- 5B1M 2.34 Å, The mouse nucleosome structure containing H3.1
- 7OS4 2.54 Å, Crystal structure of mouse CARM1 in complex with histone H3_13-31 K18
- 5IX1 2.6 Å, Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and H3K4me3…
- 2XL3 2.7 Å, WDR5 in complex with an RBBP5 peptide and histone H3 peptide
- 5IX2 2.9 Å, Crystal structure of mouse Morc3 ATPase-CW cassette in complex with AMPPNP and…
- 1U35 3.0 Å, Crystal structure of the nucleosome core particle containing the histone domain of…
- 7VFI 3.98 Å, Cryo-EM structure of the mouse TAPL (9mer-peptide bound)
- 1GUW Structure of the chromodomain from mouse HP1beta in complex with the lysine 9-methyl…
Browse structure collections
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