9GMK: SIRT7:H3K18DTU nucleosome complex
SIRT7:H3K18DTU nucleosome complex. Determined by electron microscopy at 3.5 Å resolution. Released 29 Jan 2025.
- Method
- Electron microscopy
- Resolution
- 3.5 Å
- Organism
- Homo sapiens
- Chains
- 11
- Atoms
- 14,643
- Mol. weight
- 245.89 kDa
- Released
- 29 Jan 2025
Explore 9GMK in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9GMK contains 55 α-helices and 27 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 | 41-42 | 2 | |
| α-helix | 45-56 | 12 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 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 | 31-41 | 11 | |
| β-strand | 45-46 | 2 | 2 |
| α-helix | 51-75 | 25 | |
| β-strand | 80 | 1 | 1 |
| α-helix | 83-92 | 10 | |
| β-strand | 97 | 1 | 3 |
Chain C: 5 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| α-helix | 47-72 | 26 | |
| β-strand | 77 | 1 | 4 |
| α-helix | 80-89 | 10 | |
| α-helix | 91-96 | 6 | |
| β-strand | 101 | 1 | 5 |
Chain D: 4 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| β-strand | 53 | 1 | 4 |
| α-helix | 57-83 | 27 | |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
Chain E: 5 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 41-42 | 2 | |
| α-helix | 45-54 | 10 | |
| α-helix | 64-75 | 12 | |
| β-strand | 83 | 1 | 6 |
| 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 | 31-40 | 10 | |
| α-helix | 51-75 | 25 | |
| β-strand | 80 | 1 | 6 |
| α-helix | 83-92 | 10 | |
| β-strand | 97 | 1 | 5 |
Chain G: 6 helices, 1 β-strand
| Element | Residues | Length | Sheet |
|---|
| α-helix | 17-21 | 5 | |
| α-helix | 28-35 | 8 | |
| α-helix | 47-72 | 26 | |
| α-helix | 80-88 | 9 | |
| α-helix | 91-97 | 7 | |
| β-strand | 101 | 1 | 3 |
| α-helix | 113-115 | 3 | |
Chain H: 4 helices, 0 β-strands
| Element | Residues | Length | Sheet |
|---|
| α-helix | 38-48 | 11 | |
| α-helix | 56-83 | 28 | |
| α-helix | 91-101 | 11 | |
| α-helix | 104-123 | 20 | |
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 | Homo sapiens | Q71DI3 (AlphaFold model) |
| Histone H4 | B, F | protein | 103 | Homo sapiens | P62805 (AlphaFold model) |
| Histone H2A type 2-A | C, G | protein | 129 | Homo sapiens | Q6FI13 (AlphaFold model) |
| Histone H2B type 1-J | D, H | protein | 126 | Homo sapiens | P06899 (AlphaFold model) |
| NAD-dependent protein deacetylase sirtuin-7 | K | protein | 401 | Homo sapiens | Q9NRC8 |
| DNA (148-mer) | L | DNA | 148 | Homo sapiens | |
| DNA (148-mer) | M | DNA | 148 | Homo sapiens | |
Sequence of entity 1 (A, E), FASTA
>9GMK_1 Histone H3.2 (chains A, E)
MARTKQTARKSTGGKAPRKQLATKAARKSAPATGGVKKPHRYRPGTVCLREIRRYQKSTE
LLIRKLPFQRLVREIAQDFKTDLRFQSSAVMALQEASEAYLVGLFEDTNLAAIHAKRVTI
MPKDIQLARRIRGERA
Sequence of entity 2 (B, F), FASTA
>9GMK_2 Histone H4 (chains B, F)
MSGRGKGGKGLGKGGAKRHRKVLRDNIQGITKPAIRRLARRGGVKRISGLIYEETRGVLK
VFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLYGFGG
Sequence of entity 3 (C, G), FASTA
>9GMK_3 Histone H2A type 2-A (chains C, G)
SGRGKQGGKARAKAKSRSSRAGLQFPVGRVHRLLRKGNYAERVGAGAPVYMAAVLEYLTA
EILELAGNAARDNKKTRIIPRHLQLAIRNDEELNKLLGKVTIAQGGVLPNIQAVLLPKKT
ESHHKAKGK
Sequence of entity 4 (D, H), FASTA
>9GMK_4 Histone H2B type 1-J (chains D, H)
MPEPAKSAPAPKKGSKKAVTKAQKKDGKKRKRSRKESYSIYVYKVLKQVHPDTGISSKAM
GIMNSFVNDIFERIAGEASRLAHYNKRSTITSREIQTAVRLLLPGELAKHAVSEGTKAVT
KYTSAK
Sequence of entity 5 (K), FASTA
>9GMK_5 NAD-dependent protein deacetylase sirtuin-7 (chains K)
GMAAGGLSRSERKAAERVRRLREEQQRERLRQVSRILRKAAAERSAEEGRLLAESADLVT
ELQGRSRRREGLKRRQEEVCDDPEELRGKVRELASAVRNAKYLVVYTGAGISTAASIPDY
RGPNGVWTLLQKGRSVSAADLSEAEPTLTHMSITRLHEQKLVQHVVSQNCDGLHLRSGLP
RTAISELHGNMYIEVCTSCVPNREYVRVFDVTERTALHRHQTGRTCHKCGTQLRDTIVHF
GERGTLGQPLNWEAATEAASRADTILCLGSSLKVLKKYPRLWCMTKPPSRRPKLYIVNLQ
WTPKDDWAALKLHGKCDDVMRLLMAELGLEIPAYSRWQDPIFSLATPLRAGEEGSHSRKS
LCRSREEAPPGDRGAPLSSAPILGGWFGRGCTKRTKRKKVT
Sequence of entity 6 (L), FASTA
>9GMK_6 DNA (148-MER) (chains L)
AGAATCCCGGTGCCGAGGCCGCTCAATTGGTCGTAGACAGCTCTAGCACCGCTTAAACGC
ACGTACGCGCTGTCCCCCGCGTTTTAACCGCCAAGGGGATTACTCCCTAGTCTCCAGGCA
CGTGTCAGATATATACAATTTTTTTTTT
Sequence of entity 7 (M), FASTA
>9GMK_7 DNA (148-MER) (chains M)
AAAAAAAAAATTGTATATATCTGACACGTGCCTGGAGACTAGGGAGTAATCCCCTTGGCG
GTTAAAACGCGGGGGACAGCGCGTACGTGCGTTTAAGCGGTGCTAGAGCTGTCTACGACC
AATTGAGCGGCCTCGGCACCGGGATTCT
Primary citation
Structural basis of SIRT7 nucleosome engagement and substrate specificity. Moreno-Yruela, C., Ekundayo, B.E., Foteva, P.N. et al. Nat Commun (2025) 16:1328-1328. DOI 10.1038/s41467-025-56529-y · PubMed
Other PDB entries of the same protein (UniProt Q71DI3 (AlphaFold model), which also has an AlphaFold model), best resolution first:
- 2X4W 1.5 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4MZG 1.7 Å, Crystal structure of human Spindlin1 bound to histone H3K4me3 peptide
- 2X4Y 1.7 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 2X4X 1.85 Å, Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.
- 4OUC 1.9 Å, Structure of human haspin in complex with histone H3 substrate
- 5VAC 1.95 Å, Crystal Structure of ATXR5 SET domain in complex with K36me3 histone H3 peptide
- 6ACE 1.98 Å, histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122
- 7UVA 1.98 Å, Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36…
- 5B0Z 1.99 Å, The crystal structure of the nucleosome containing H3.2, at 1.98 A resolution
- 3R93 2.06 Å, Crystal structure of the chromo domain of M-phase phosphoprotein 8 bound to H3K9Me3…
- 4MZF 2.1 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2a) peptide
- 4MZH 2.2 Å, Crystal structure of human Spindlin1 bound to histone H3(K4me3-R8me2s) peptide
Browse structure collections
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