7K5Y: Histone H3.1
Cryo-EM structure of a chromatosome containing human linker histone H1.4. Determined by electron microscopy at 2.76 Å resolution. Released 25 Nov 2020.
- Method
- Electron microscopy
- Resolution
- 2.76 Å
- Organisms
- Homo sapiens, Mus musculus
- Chains
- 13
- Atoms
- 18,258
- Mol. weight
- 312.14 kDa
- Released
- 25 Nov 2020
Explore 7K5Y in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7K5Y contains 55 α-helices and 69 β-strands across 11 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 | 64-76 | 13 | |
| 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 | 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: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 11-13 | 3 | |
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| 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 | 101-102 | 2 | 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 | 104-122 | 19 | |
Chain F: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| 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: 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 | 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 | |
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 | 105-123 | 19 | |
Chain M: 5 helices, 23 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 23-25 | 3 | 11 |
| β-strand | 29-32 | 4 | 12 |
| β-strand | 38-44 | 7 | 11 |
| β-strand | 52-57 | 6 | 12 |
| β-strand | 64-68 | 5 | 12 |
| β-strand | 72-73 | 2 | 12 |
| α-helix | 74 | 1 | |
| β-strand | 81-86 | 6 | 11 |
| β-strand | 89-94 | 6 | 11 |
| α-helix | 99-101 | 3 | |
| β-strand | 103-109 | 7 | 12 |
| β-strand | 116-117 | 2 | 12 |
| β-strand | 121-125 | 5 | 12 |
| β-strand | 152-155 | 4 | 13 |
| β-strand | 159-161 | 3 | 12 |
| β-strand | 167-174 | 8 | 13 |
| α-helix | 178-180 | 3 | |
| β-strand | 181-189 | 9 | 12 |
| β-strand | 193-201 | 9 | 12 |
| β-strand | 206-209 | 4 | 12 |
| α-helix | 211-213 | 3 | |
| β-strand | 214 | 1 | 13 |
| β-strand | 217-222 | 6 | 13 |
| β-strand | 227-232 | 6 | 13 |
| α-helix | 237-239 | 3 | |
| β-strand | 241-249 | 9 | 12 |
| β-strand | 258-259 | 2 | 12 |
| β-strand | 263-267 | 5 | 12 |
2 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| Histone H3.1 | A, E | protein | 136 | Homo sapiens | P68431 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 1-B/E | C, G | protein | 130 | Homo sapiens | P04908 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| DNA (197-mer) | I | DNA | 197 | Homo sapiens | |
| DNA (197-mer) | J | DNA | 197 | Homo sapiens | |
| scFv20 | M, N | protein | 270 | Mus musculus | |
| Histone H1.4 | U | protein | 219 | Homo sapiens | P10412 |
Sequence of entity 1 (A, E), FASTA
>7K5Y_1 Histone H3.1 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEACEAYLVGLFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>7K5Y_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>7K5Y_3 Histone H2A type 1-B/E (chains C, G)
MSGRGKQGGKARAKAKTRSSRAGLQFPVGRVHRLLRKGNYSERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGRVTIAQGGVLPNIQAVLLPKK
TESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>7K5Y_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (I), FASTA
>7K5Y_5 DNA (197-MER) (chains I)
GGGCTGGACCCTATACGCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGT
CGTAGACAGCTCTAGCACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGC
CAAGGGGATTACTCCCTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTAT
TGAACAGCGACCACCCC
Sequence of entity 6 (J), FASTA
>7K5Y_6 DNA (197-MER) (chains J)
GGGGTGGTCGCTGTTCAATACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACT
AGGGAGTAATCCCCTTGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGG
TGCTAGAGCTGTCTACGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCG
CGTATAGGGTCCAGCCC
Sequence of entity 7 (M, N), FASTA
>7K5Y_7 scFv20 (chains M, N)
MKSSHHHHHHENLYFQSNAMDIKMTQSPSSMHASLGERVTITCKASQDIRSYLSWYQQKP
WKSPKTLIYYATSLADGVPSRFSGSGSGQDFSLTINNLESDDTATYYCLQHGESPYTFGS
GTKLEIKRAGGGGSGGGGSGGGGSGGGGSMEVQLQQSGPELVEPGTSVKMPCKASGYTFT
SYTIQWVKQTPRQGLEWIGYIYPYNAGTKYNEKFKGKATLTSDKSSSTVYMELSSLTSED
SAVYYCARKSSRLRSTLDYWGQGTSVTVSS
Sequence of entity 8 (U), FASTA
>7K5Y_8 Histone H1.4 (chains U)
MSETAPAAPAAPAPAEKTPVKKKARKSAGAAKRKASGPPVSELITKAVAASKERSGVSLA
ALKKALAAAGYDVEKNNSRIKLGLKSLVSKGTLVQTKGTGASGSFKLNKKAASGEAKPKA
KKAGAAKAKKPAGAAKKPKKATGAATPKKSAKKTPKKAKKPAAAAGAKKAKSPKKAKAAK
PKKAPKSPAKAKAVKPKAAKPKTAKPKAAKPKKAAAKKK
Primary citation
Distinct Structures and Dynamics of Chromatosomes with Different Human Linker Histone Isoforms. Zhou, B.R., Feng, H., Kale, S. et al. Mol Cell (2021) 81:166-182.e6. DOI 10.1016/j.molcel.2020.10.038 · PubMed
Other PDB entries of the same protein (UniProt P68431 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 5SVY 1.05 Å, MORC3 CW in complex with histone H3K4me1
- 2V89 1.1 Å, Crystal structure of RAG2-PHD finger in complex with H3K4me3 peptide at 1.1A resolution
- 5SZC 1.19 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 5SZB 1.2 Å, Structure of human Dpf3 double-PHD domain bound to histone H3 tail peptide with…
- 6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 4UP0 1.28 Å, Ternary crystal structure of the Pygo2 PHD finger in complex with the B9L HD1 domain and…
- 5WXH 1.3 Å, Crystal structure of TAF3 PHD finger bound to H3K4me3
- 5FFV 1.3 Å, Crystal structure of the bromodomain of human BRPF1 in complex with H3K14ac histone…
- 4L7X 1.35 Å, Crystal structure of the DIDO PHD finger in complex with H3K4me3
- 6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
- 3ASL 1.41 Å, Structure of UHRF1 in complex with histone tail
Browse structure collections
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