7XYG: Fft3-nucleosome complex with Fft3
Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome. Determined by electron microscopy at 4.2 Å resolution. Released 6 Dec 2023.
- Method
- Electron microscopy
- Resolution
- 4.2 Å
- Organisms
- Drosophila melanogaster, synthetic construct, Schizosaccharomyces pombe 972h-
- Chains
- 11
- Atoms
- 17,273
- Mol. weight
- 315.11 kDa
- Released
- 6 Dec 2023
Explore 7XYG in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
7XYG contains 69 α-helices and 30 β-strands across 9 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 | 39-42 | 4 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83-84 | 2 | 10 |
| α-helix | 86-113 | 28 | |
| β-strand | 118 | 1 | 11 |
| α-helix | 121-130 | 10 | |
Chain B: 4 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-27 | 3 | |
| α-helix | 31-40 | 10 | |
| β-strand | 45 | 1 | 11 |
| α-helix | 50-75 | 26 | |
| β-strand | 80-81 | 2 | 10 |
| α-helix | 84-93 | 10 | |
| β-strand | 97-98 | 2 | 6 |
Chain C: 7 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-20 | 4 | |
| α-helix | 27-36 | 10 | |
| β-strand | 42-43 | 2 | 1 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 2 |
| α-helix | 79 | 1 | |
| α-helix | 80-87 | 8 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 3 |
| α-helix | 117-118 | 2 | |
Chain D: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-45 | 11 | |
| β-strand | 50-51 | 2 | 2 |
| α-helix | 53-80 | 28 | |
| β-strand | 85-86 | 2 | 1 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-119 | 19 | |
Chain E: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 45-56 | 12 | |
| α-helix | 64-78 | 15 | |
| α-helix | 86-113 | 28 | |
| α-helix | 121-130 | 10 | |
Chain F: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-40 | 10 | |
| α-helix | 53-76 | 24 | |
| α-helix | 83-92 | 10 | |
| β-strand | 96-97 | 2 | 3 |
Chain G: 5 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-35 | 9 | |
| β-strand | 42 | 1 | 4 |
| α-helix | 46-72 | 27 | |
| β-strand | 77-78 | 2 | 5 |
| α-helix | 80-88 | 9 | |
| α-helix | 92-96 | 5 | |
| β-strand | 101-102 | 2 | 6 |
Chain H: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 35-43 | 9 | |
| β-strand | 50-51 | 2 | 5 |
| α-helix | 53-80 | 28 | |
| β-strand | 85 | 1 | 4 |
| α-helix | 88-98 | 11 | |
| α-helix | 101-111 | 11 | |
| α-helix | 115-119 | 5 | |
1 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 H2A | C, G | protein | 123 | Drosophila melanogaster | P84051 (AlphaFold model) |
| Histone H2B | D, H | protein | 123 | Drosophila melanogaster | P02283 (AlphaFold model) |
| DNA (167-mer) | J | DNA | 167 | synthetic construct | |
| DNA (167-mer) | I | DNA | 167 | synthetic construct | |
| ATP-dependent helicase fft3 | K | protein | 922 | Schizosaccharomyces pombe 972h- | O42861 (AlphaFold model) |
| Histone H3 | A, E | protein | 135 | Drosophila melanogaster | P02299 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Drosophila melanogaster | P84040 |
Sequence of entity 1 (C, G), FASTA
>7XYG_1 Histone H2A (chains C, G)
SGRGKGGKVKGKAKSRSNRAGLQFPVGRIHRLLRKGNYAERVGAGAPVYLAAVMEYLAAE
VLELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLSGVTIAQGGVLPNIQAVLLPKKTE
KKA
Sequence of entity 2 (D, H), FASTA
>7XYG_2 Histone H2B (chains D, H)
MPPKTSGKAAKKAGKAQKNITKTDKKKKRKRKESYAIYIYKVLKQVHPDTGISSKAMSIM
NSFVNDIFERIAAEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SSK
Sequence of entity 3 (J), FASTA
>7XYG_3 DNA (167-MER) (chains J)
ATCTACATGCACAGGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCT
TGGCGGTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTA
CGACCAATTGAGCGGCCTCGGCACCGGGATTCTCCAGGGCGGCCGAT
Sequence of entity 4 (I), FASTA
>7XYG_4 DNA (167-MER) (chains I)
ATCGGCCGCCCTGGAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAG
CACCGCTTAAACGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCC
CTAGTCTCCAGGCACGTGTCAGATATATACATCCTGTGCATGTAGAT
Sequence of entity 5 (K), FASTA
>7XYG_5 ATP-dependent helicase fft3 (chains K)
MDGKRKIEHTADGTHYDATSNVKRKPIFPPFIADSLSEATEKANVMGGGMNSRLQILSEM
SKRVQATAPISSLEHFKQLSDISPSFTSSANSINQPYNYSGSLENLVPTPSAGTPSQFMD
AQNPYGAVYNALSQFSETEPKMPSYMDDEEASDSLPLSLSSQSLSSQVTNQKPAPHRLTM
RERYAANNLTNGLQFTLPLSSRKTYEPEADDDSNDDMYSDDDSNADRWASRIDTAALKEE
VLKYMNRCSTQDLADMTGCTLAEAEFMVAKRPFPDLESALVVKQPRPVIPKGRRGRREKT
PLGPRLVGICMEIMRGYFVVDALIRQCEQLGGKIQRGIEAWGLSNTATSDEGETSLVNFD
QMKSFGTPANSSFITTPPASFSPDIKLQDYQIIGINWLYLLYELKLAGILADEMGLGKTC
QTIAFFSLLMDKNINGPHLVIAPASTMENWLREFAKFCPKLKIELYYGSQVEREEIRERI
NSNKDSYNVMLTTYRLAATSKADRLFLRNQKFNVCVYDEGHYLKNRASERYRHLMSIPAD
FRVLLTGTPLQNNLKELISLLAFILPHVFDYGLKSLDVIFTMKKSPESDFERALLSEQRV
SRAKMMMAPFVLRRKKSQVLDALPKKTRIIEFCEFSEEERRRYDDFASKQSVNSLLDENV
MKTNLDTNANLAKKKSTAGFVLVQLRKLADHPMLFRIHYKDDILRQMAKAIMNEPQYKKA
NELYIFEDMQYMSDIELHNLCCKFPSINSFQLKDEPWMDATKVRKLKKLLTNAVENGDRV
VLFSQFTQVLDILQLVMKSLNLKFLRFDGSTQVDFRQDLIDQFYADESINVFLLSTKAGG
FGINLACANMVILYDVSFNPFDDLQAEDRAHRVGQKKEVTVYKFVVKDTIEEHIQRLANA
KIALDATLSGNAETVEAEDDDD
Sequence of entity 6 (A, E), FASTA
>7XYG_6 Histone H3 (chains A, E)
ARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTEL
LIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLCAIHAKRVTIM
PKDIQLARRIRGERA
Sequence of entity 7 (B, F), FASTA
>7XYG_7 Histone H4 (chains B, F)
MTGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Primary citation
Cryo-EM structure of Fft3-nucleosome complex with Fft3 bound to SHL+3 position of the nucleosome (Class II Fft3-nucleosome complex). Nan, Z., Tao, J., Yangao, H. To be published.
Other PDB entries of the same protein (UniProt P84051 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 9ZQB 2.1 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 1
- 2NQB 2.3 Å, Drosophila Nucleosome Structure
- 9ZQC 2.37 Å, Nucleosome with an SSB at SHL -2.8 in complex with human PARP2 and HPF1, Class 2
- 2PYO 2.43 Å, Drosophila nucleosome core
- 8UX1 2.5 Å, Cryo-EM structure of Ran bound to RCC1 and the nucleosome core particle
- 8PP7 2.91 Å, human RYBP-PRC1 bound to mononucleosome
- 6DZT 2.99 Å, Cryo-EM structure of nucleosome in complex with a single chain antibody fragment
- 8PP6 3.18 Å, human RYBP-PRC1 bound to H2AK118ub1 nucleosome
- 9ZQA 3.28 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 2
- 9MU4 3.29 Å, Structure of a native Drosophila melanogaster octameric nucleosome
- 9ZQ9 3.3 Å, Nucleosome with an SSB at SHL -2.8 in complex with the WGR domain of human PARP2, Class 1
- 4X23 3.5 Å, Crystal structure of cenp-C in complex with the nucleosome core particle
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