5O9G: Nucleosome-Chd1 complex
Structure of nucleosome-Chd1 complex. Determined by electron microscopy at 4.8 Å resolution. Released 11 Oct 2017.
- Method
- Electron microscopy
- Resolution
- 4.8 Å
- Organisms
- Xenopus laevis, synthetic construct, Saccharomyces cerevisiae S288c
- Chains
- 11
- Atoms
- 19,681
- Mol. weight
- 406.49 kDa
- Ligands
- ADP, BEF
- Released
- 11 Oct 2017
Explore 5O9G in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
5O9G contains 79 α-helices and 39 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, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-55 | 11 | |
| α-helix | 64-78 | 15 | |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain B: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 25-28 | 4 | |
| α-helix | 31-41 | 11 | |
| α-helix | 51-75 | 25 | |
| α-helix | 84-92 | 9 | |
| β-strand | 96-97 | 2 | 1 |
Chain C: 7 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-36 | 9 | |
| α-helix | 47-72 | 26 | |
| β-strand | 77-78 | 2 | 2 |
| α-helix | 79 | 1 | |
| α-helix | 80-87 | 8 | |
| α-helix | 92-96 | 5 | |
| β-strand | 100-101 | 2 | 3 |
| α-helix | 113-115 | 3 | |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-43 | 6 | |
| β-strand | 50-51 | 2 | 2 |
| α-helix | 53-80 | 28 | |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
Chain E: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-78 | 15 | |
| β-strand | 84 | 1 | 4 |
| α-helix | 86-113 | 28 | |
| α-helix | 121-131 | 11 | |
Chain F: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 26-28 | 3 | |
| α-helix | 31-41 | 11 | |
| α-helix | 51-75 | 25 | |
| β-strand | 81 | 1 | 4 |
| α-helix | 84-93 | 10 | |
| β-strand | 96-97 | 2 | 3 |
Chain G: 6 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 27-36 | 10 | |
| β-strand | 43 | 1 | 5 |
| α-helix | 47-71 | 25 | |
| β-strand | 77-78 | 2 | 6 |
| α-helix | 80-88 | 9 | |
| α-helix | 91-96 | 6 | |
| β-strand | 100-101 | 2 | 1 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 36-42 | 7 | |
| β-strand | 50-51 | 2 | 6 |
| α-helix | 53-80 | 28 | |
| β-strand | 86 | 1 | 5 |
| α-helix | 88-98 | 11 | |
| α-helix | 102-120 | 19 | |
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 H3.2 | A, E | protein | 136 | Xenopus laevis | P84233 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Xenopus laevis | P62799 (AlphaFold model) |
| Histone H2A | C, G | protein | 130 | Xenopus laevis | P06897 (AlphaFold model) |
| Histone H2B 1.1 | D | protein | 123 | Xenopus laevis | P02281 (AlphaFold model) |
| Histone H2B 1.1 | H | protein | 122 | Xenopus laevis | P02281 (AlphaFold model) |
| DNA (162-mer) | I | DNA | 208 | synthetic construct | |
| DNA (162-mer) | J | DNA | 208 | synthetic construct | |
| Chromo domain-containing protein 1 | W | protein | 1468 | Saccharomyces cerevisiae S288c | P32657 |
Sequence of entity 1 (A, E), FASTA
>5O9G_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVALREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVALFEDTNLCAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>5O9G_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>5O9G_3 Histone H2A (chains C, G)
MSGRGKQGGKTRAKAKTRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYLAAVLEYLT
AEILELAGNAARDNKKTRIIPRHLQLAVRNDEELNKLLGRVTIAQGGVLPNIQSVLLPKK
TESSKSAKSK
Sequence of entity 4 (D), FASTA
>5O9G_4 Histone H2B 1.1 (chains D)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SAK
Sequence of entity 5 (H), FASTA
>5O9G_5 Histone H2B 1.1 (chains H)
MAKSAPAPKKGSKKAVTKTQKKDGKKRRKTRKESYAIYVYKVLKQVHPDTGISSKAMSIM
NSFVNDVFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVTKYT
SA
Sequence of entity 6 (I), FASTA
>5O9G_6 DNA (162-MER) (chains I)
ATCAGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAA
CGCACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAG
GCACGTGTCAGATATATACATCGATTAACGATGCTGGGCATAAGCGTGGTTCAATACCGG
CGCATAAAGGGTAAATTCGAAAACAGCG
Sequence of entity 7 (J), FASTA
>5O9G_7 DNA (162-MER) (chains J)
CGCTGTTTTCGAATTTACCCTTTATGCGCCGGTATTGAACCACGCTTATGCCCAGCATCG
TTAATCGATGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCGGTT
AAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACCAAT
TGAGCGGCCTCGGCACCGGGATTCTGAT
Sequence of entity 8 (W), FASTA
>5O9G_8 Chromo domain-containing protein 1 (chains W)
MAAKDISTEVLQNPELYGLRRSHRAAAHQQNYFNDSDDEDDEDNIKQSRRKRMTTIEDDE
DEFEDEEGEEDSGEDEDEEDFEEDDDYYGSPIKQNRSKPKSRTKSKSKSKPKSQSEKQST
VKIPTRFSNRQNKTVNYNIDYSDDDLLESEDDYGSEEALSEENVHEASANPQPEDFHGID
IVINHRLKTSLEEGKVLEKTVPDLNNCKENYEFLIKWTDESHLHNTWETYESIGQVRGLK
RLDNYCKQFIIEDQQVRLDPYVTAEDIEIMDMERERRLDEFEEFHVPERIIDSQRASLED
GTSQLQYLVKWRRLNYDEATWENATDIVKLAPEQVKHFQNRENSKILPQYSSNYTSQRPR
FEKLSVQPPFIKGGELRDFQLTGINWMAFLWSKGDNGILADEMGLGKTVQTVAFISWLIF
ARRQNGPHIIVVPLSTMPAWLDTFEKWAPDLNCICYMGNQKSRDTIREYEFYTNPRAKGK
KTMKFNVLLTTYEYILKDRAELGSIKWQFMAVDEAHRLKNAESSLYESLNSFKVANRMLI
TGTPLQNNIKELAALVNFLMPGRFTIDQEIDFENQDEEQEEYIHDLHRRIQPFILRRLKK
DVEKSLPSKTERILRVELSDVQTEYYKNILTKNYSALTAGAKGGHFSLLNIMNELKKASN
HPYLFDNAEERVLQKFGDGKMTRENVLRGLIMSSGKMVLLDQLLTRLKKDGHRVLIFSQM
VRMLDILGDYLSIKGINFQRLDGTVPSAQRRISIDHFNSPDSNDFVFLLSTRAGGLGINL
MTADTVVIFDSDWNPQADLQAMARAHRIGQKNHVMVYRLVSKDTVEEEVLERARKKMILE
YAIISLGVTDGNKYTKKNEPNAGELSAILKFGAGNMFTATDNQKKLEDLNLDDVLNHAED
HVTTPDLGESHLGGEEFLKQFEVTDYKADIDWDDIIPEEELKKLQDEEQKRKDEEYVKEQ
LEMMNRRDNALKKIKNSVNGDGTAANSDSDDDSTSRSSRRRARANDMDSIGESEVRALYK
AILKFGNLKEILDELIADGTLPVKSFEKYGETYDEMMEAAKDCVHEEEKNRKEILEKLEK
HATAYRAKLKSGEIKAENQPKDNPLTRLSLKKREKKAVLFNFKGVKSLNAESLLSRVEDL
KYLKNLINSNYKDDPLKFSLGNNTPKPVQNWSSNWTKEEDEKLLIGVFKYGYGSWTQIRD
DPFLGITDKIFLNEVHNPVAKKSASSSDTTPTPSKKGKGITGSSKKVPGAIHLGRRVDYL
LSFLRGGLNTKSPSADIGSKKLPTGPSKKRQRKPANHSKSMTPEITSSEPANGPPSKRMK
ALPKGPAALINNTRLSPNSPTPPLKSKVSRDNGTRQSSNPSSGSAHEKEYDSMDEEDCRH
TMSAIRTSLKRLRRGGKSLDRKEWAKILKTELTTIGNHIESQKGSSRKASPEKYRKHLWS
YSANFWPADVKSTKLMAMYDKITESQKK
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| ADP | Adenosine-5'-diphosphate | C10 H15 N5 O10 P2 | 1 |
| BEF | Beryllium trifluoride ion | Be F3 | 1 |
Primary citation
Nucleosome-Chd1 structure and implications for chromatin remodelling. Farnung, L., Vos, S.M., Wigge, C. et al. Nature (2017) 550:539-542. DOI 10.1038/nature24046 · PubMed
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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