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Open data
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Basic information
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| Title | SIRT7:H3K18DTU nucleosome complex | |||||||||||||||
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Keywords | nucleosome complex / DNA | |||||||||||||||
| Function / homology | Function and homology informationregulation of transcription of nucleolar large rRNA by RNA polymerase I / nucleolus organizer region / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / protein deglutarylation / protein-glutaryllysine deglutarylase activity / histone H3K18 deacetylase activity, NAD-dependent / protein-succinyllysine desuccinylase activity / R-loop processing / homologous chromosome pairing at meiosis ...regulation of transcription of nucleolar large rRNA by RNA polymerase I / nucleolus organizer region / protein depropionylation / NAD-dependent protein-lysine depropionylase activity / protein deglutarylation / protein-glutaryllysine deglutarylase activity / histone H3K18 deacetylase activity, NAD-dependent / protein-succinyllysine desuccinylase activity / R-loop processing / homologous chromosome pairing at meiosis / protein methyltransferase activity / transposable element silencing / NAD-dependent protein lysine deacetylase activity / protein acetyllysine N-acetyltransferase / positive regulation of rRNA processing / regulation of protein export from nucleus / protein deacetylation / regulation of mitochondrion organization / DNA repair-dependent chromatin remodeling / positive regulation of transcription by RNA polymerase I / rRNA transcription / NAD+ binding / negative regulation of tumor necrosis factor-mediated signaling pathway / regulation of DNA repair / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / CENP-A containing nucleosome / Packaging Of Telomere Ends / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / negative regulation of protein ubiquitination / positive regulation of gluconeogenesis / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Deposition of new CENPA-containing nucleosomes at the centromere / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / telomere organization / Interleukin-7 signaling / transcription initiation-coupled chromatin remodeling / Inhibition of DNA recombination at telomere / RNA Polymerase I Promoter Opening / Meiotic synapsis / Assembly of the ORC complex at the origin of replication / SUMOylation of chromatin organization proteins / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / innate immune response in mucosa / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / HDACs deacetylate histones / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / HDMs demethylate histones / G2/M DNA damage checkpoint / NoRC negatively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / B-WICH complex positively regulates rRNA expression / PKMTs methylate histone lysines / Meiotic recombination / Pre-NOTCH Transcription and Translation / Metalloprotease DUBs / RMTs methylate histone arginines / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of granulopoiesis / HCMV Early Events / antimicrobial humoral immune response mediated by antimicrobial peptide / osteoblast differentiation / structural constituent of chromatin / UCH proteinases / antibacterial humoral response / nucleosome / heterochromatin formation / nucleosome assembly / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / site of double-strand break / HATs acetylate histones / RUNX1 regulates transcription of genes involved in differentiation of HSCs / Factors involved in megakaryocyte development and platelet production / chromatin organization / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / Oxidative Stress Induced Senescence / defense response to Gram-negative bacterium Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||||||||
Authors | Moreno-Yruela C / Ekundayo B / Foteva P / Calvino-Sanles E / Ni D / Stahlberg H / Fierz B | |||||||||||||||
| Funding support | Switzerland, Denmark, Spain, 4 items
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Citation | Journal: Nat Commun / Year: 2025Title: Structural basis of SIRT7 nucleosome engagement and substrate specificity. Authors: Carlos Moreno-Yruela / Babatunde E Ekundayo / Polina N Foteva / Dongchun Ni / Esther Calvino-Sanles / Henning Stahlberg / Beat Fierz / ![]() Abstract: Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD-dependent deacylase often deregulated in cancer, which deacetylates either ...Chromatin-modifying enzymes target distinct residues within histones to finetune gene expression profiles. SIRT7 is an NAD-dependent deacylase often deregulated in cancer, which deacetylates either H3 lysine 36 (H3K36) or H3K18 with high specificity within nucleosomes. Here, we report structures of nucleosome-bound SIRT7, and uncover the structural basis of its specificity towards H3K36 and K18 deacylation, combining a mechanism-based cross-linking strategy, cryo-EM, and enzymatic and cellular assays. We show that the SIRT7 N-terminus represents a unique, extended nucleosome-binding domain, reaching across the nucleosomal surface to the acidic patch. The catalytic domain binds at the H3-tail exit site, engaging both DNA gyres of the nucleosome. Contacting H3K36 versus H3K18 requires a change in binding pose, and results in structural changes in both SIRT7 and the nucleosome. These structures reveal the basis of lysine specificity, allowing us to engineer SIRT7 towards enhanced H3K18ac selectivity, and provides a basis for small molecule modulator development. | |||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_51449.map.gz | 26.5 MB | EMDB map data format | |
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| Header (meta data) | emd-51449-v30.xml emd-51449.xml | 28.6 KB 28.6 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_51449_fsc.xml | 7.9 KB | Display | FSC data file |
| Images | emd_51449.png | 100.9 KB | ||
| Filedesc metadata | emd-51449.cif.gz | 7.7 KB | ||
| Others | emd_51449_half_map_1.map.gz emd_51449_half_map_2.map.gz | 48.9 MB 48.9 MB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-51449 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-51449 | HTTPS FTP |
-Validation report
| Summary document | emd_51449_validation.pdf.gz | 1 MB | Display | EMDB validaton report |
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| Full document | emd_51449_full_validation.pdf.gz | 1 MB | Display | |
| Data in XML | emd_51449_validation.xml.gz | 15.8 KB | Display | |
| Data in CIF | emd_51449_validation.cif.gz | 20.4 KB | Display | |
| Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51449 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-51449 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9gmkMC ![]() 9gmrC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_51449.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.089 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #1
| File | emd_51449_half_map_1.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
-Half map: #2
| File | emd_51449_half_map_2.map | ||||||||||||
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| Projections & Slices |
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| Density Histograms |
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Sample components
-Entire : K18 structure
| Entire | Name: K18 structure |
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| Components |
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-Supramolecule #1: K18 structure
| Supramolecule | Name: K18 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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| Source (natural) | Organism: Homo sapiens (human) |
-Macromolecule #1: Histone H3.2
| Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 15.421101 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVCLR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA UniProtKB: Histone H3.2 |
-Macromolecule #2: Histone H4
| Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 11.394426 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #3: Histone H2A type 2-A
| Macromolecule | Name: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 13.994354 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY MAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK UniProtKB: Histone H2A type 2-A |
-Macromolecule #4: Histone H2B type 1-J
| Macromolecule | Name: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 13.935239 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KRSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK UniProtKB: Histone H2B type 1-J |
-Macromolecule #5: NAD-dependent protein deacetylase sirtuin-7
| Macromolecule | Name: NAD-dependent protein deacetylase sirtuin-7 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein acetyllysine N-acetyltransferase |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 45.03559 KDa |
| Recombinant expression | Organism: ![]() |
| Sequence | String: GMAAGGLSRS ERKAAERVRR LREEQQRERL RQVSRILRKA AAERSAEEGR LLAESADLVT ELQGRSRRRE GLKRRQEEVC DDPEELRGK VRELASAVRN AKYLVVYTGA GISTAASIPD YRGPNGVWTL LQKGRSVSAA DLSEAEPTLT HMSITRLHEQ K LVQHVVSQ ...String: GMAAGGLSRS ERKAAERVRR LREEQQRERL RQVSRILRKA AAERSAEEGR LLAESADLVT ELQGRSRRRE GLKRRQEEVC DDPEELRGK VRELASAVRN AKYLVVYTGA GISTAASIPD YRGPNGVWTL LQKGRSVSAA DLSEAEPTLT HMSITRLHEQ K LVQHVVSQ NCDGLHLRSG LPRTAISELH GNMYIEVCTS CVPNREYVRV FDVTERTALH RHQTGRTCHK CGTQLRDTIV HF GERGTLG QPLNWEAATE AASRADTILC LGSSLKVLKK YPRLWCMTKP PSRRPKLYIV NLQWTPKDDW AALKLHGKCD DVM RLLMAE LGLEIPAYSR WQDPIFSLAT PLRAGEEGSH SRKSLCRSRE EAPPGDRGAP LSSAPILGGW FGRGCTKRTK RKKV T UniProtKB: NAD-dependent protein deacetylase sirtuin-7 |
-Macromolecule #6: DNA (148-MER)
| Macromolecule | Name: DNA (148-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 45.428945 KDa |
| Sequence | String: (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG) (DC)(DT)(DC)(DT)(DA)(DG) ...String: (DA)(DG)(DA)(DA)(DT)(DC)(DC)(DC)(DG)(DG) (DT)(DG)(DC)(DC)(DG)(DA)(DG)(DG)(DC)(DC) (DG)(DC)(DT)(DC)(DA)(DA)(DT)(DT)(DG) (DG)(DT)(DC)(DG)(DT)(DA)(DG)(DA)(DC)(DA) (DG) (DC)(DT)(DC)(DT)(DA)(DG)(DC)(DA) (DC)(DC)(DG)(DC)(DT)(DT)(DA)(DA)(DA)(DC) (DG)(DC) (DA)(DC)(DG)(DT)(DA)(DC)(DG) (DC)(DG)(DC)(DT)(DG)(DT)(DC)(DC)(DC)(DC) (DC)(DG)(DC) (DG)(DT)(DT)(DT)(DT)(DA) (DA)(DC)(DC)(DG)(DC)(DC)(DA)(DA)(DG)(DG) (DG)(DG)(DA)(DT) (DT)(DA)(DC)(DT)(DC) (DC)(DC)(DT)(DA)(DG)(DT)(DC)(DT)(DC)(DC) (DA)(DG)(DG)(DC)(DA) (DC)(DG)(DT)(DG) (DT)(DC)(DA)(DG)(DA)(DT)(DA)(DT)(DA)(DT) (DA)(DC)(DA)(DA)(DT)(DT) (DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT) |
-Macromolecule #7: DNA (148-MER)
| Macromolecule | Name: DNA (148-MER) / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA |
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| Source (natural) | Organism: Homo sapiens (human) |
| Molecular weight | Theoretical: 45.93232 KDa |
| Sequence | String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DT)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT) (DA)(DG)(DG)(DG)(DA)(DG) ...String: (DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA)(DA) (DT)(DT)(DG)(DT)(DA)(DT)(DA)(DT)(DA)(DT) (DC)(DT)(DG)(DA)(DC)(DA)(DC)(DG)(DT) (DG)(DC)(DC)(DT)(DG)(DG)(DA)(DG)(DA)(DC) (DT) (DA)(DG)(DG)(DG)(DA)(DG)(DT)(DA) (DA)(DT)(DC)(DC)(DC)(DC)(DT)(DT)(DG)(DG) (DC)(DG) (DG)(DT)(DT)(DA)(DA)(DA)(DA) (DC)(DG)(DC)(DG)(DG)(DG)(DG)(DG)(DA)(DC) (DA)(DG)(DC) (DG)(DC)(DG)(DT)(DA)(DC) (DG)(DT)(DG)(DC)(DG)(DT)(DT)(DT)(DA)(DA) (DG)(DC)(DG)(DG) (DT)(DG)(DC)(DT)(DA) (DG)(DA)(DG)(DC)(DT)(DG)(DT)(DC)(DT)(DA) (DC)(DG)(DA)(DC)(DC) (DA)(DA)(DT)(DT) (DG)(DA)(DG)(DC)(DG)(DG)(DC)(DC)(DT)(DC) (DG)(DG)(DC)(DA)(DC)(DC) (DG)(DG)(DG) (DA)(DT)(DT)(DC)(DT) |
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Concentration | 1 mg/mL |
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| Buffer | pH: 8 |
| Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Specialist optics | Energy filter - Name: TFS Selectris X |
| Image recording | Film or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | C2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
| Refinement | Space: REAL / Protocol: AB INITIO MODEL |
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| Output model | ![]() PDB-9gmk: |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
Switzerland,
Denmark,
Spain, 4 items
Citation












Z (Sec.)
Y (Row.)
X (Col.)





































FIELD EMISSION GUN

