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- PDB-8of4: Nucleosome Bound human SIRT6 (Composite) -

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Basic information

Entry
Database: PDB / ID: 8of4
TitleNucleosome Bound human SIRT6 (Composite)
Components
  • (DNA (145-MER)) x 2
  • Histone H2A type 1
  • Histone H2B
  • Histone H3.2
  • Histone H4
  • NAD-dependent protein deacylase sirtuin-6
KeywordsGENE REGULATION / Transferase / Deacetylase / Histone H3 deacetylation
Function / homology
Function and homology information


histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin ...histone H3K56 deacetylase activity, NAD-dependent / ketone biosynthetic process / histone H3K18 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, hydrolytic mechanism / histone H3K9 deacetylase activity, NAD-dependent / protein delipidation / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / chromosome, subtelomeric region / positive regulation of protein localization to chromatin / NAD+-protein-arginine ADP-ribosyltransferase activity / pericentric heterochromatin formation / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / positive regulation of stem cell differentiation / DNA damage sensor activity / negative regulation of D-glucose import across plasma membrane / positive regulation of chondrocyte proliferation / cardiac muscle cell differentiation / transposable element silencing / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / histone deacetylase activity, NAD-dependent / positive regulation of blood vessel branching / protein localization to site of double-strand break / positive regulation of stem cell proliferation / protein deacetylation / positive regulation of vascular endothelial cell proliferation / negative regulation of glycolytic process / negative regulation of protein import into nucleus / TORC2 complex binding / regulation of protein secretion / regulation of double-strand break repair via homologous recombination / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / NAD+-protein mono-ADP-ribosyltransferase activity / lncRNA binding / negative regulation of transcription elongation by RNA polymerase II / negative regulation of cellular senescence / positive regulation of double-strand break repair / Transferases; Glycosyltransferases; Pentosyltransferases / positive regulation of telomere maintenance / regulation of lipid metabolic process / NAD+ poly-ADP-ribosyltransferase activity / NAD+ binding / DNA repair-dependent chromatin remodeling / subtelomeric heterochromatin formation / negative regulation of gluconeogenesis / positive regulation of fat cell differentiation / response to UV / pericentric heterochromatin / regulation of protein localization to plasma membrane / nucleosome binding / determination of adult lifespan / site of DNA damage / nucleotidyltransferase activity / negative regulation of protein localization to chromatin / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of protein export from nucleus / circadian regulation of gene expression / innate immune response in mucosa / protein import into nucleus / protein destabilization / chromatin DNA binding / base-excision repair / regulation of circadian rhythm / positive regulation of fibroblast proliferation / Pre-NOTCH Transcription and Translation / positive regulation of insulin secretion / glucose homeostasis / structural constituent of chromatin / transcription corepressor activity / nucleosome / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / nucleosome assembly / positive regulation of cold-induced thermogenesis / antimicrobial humoral immune response mediated by antimicrobial peptide / site of double-strand break / antibacterial humoral response / chromatin organization / heterochromatin formation / Processing of DNA double-strand break ends / damaged DNA binding / chromatin remodeling / protein heterodimerization activity / negative regulation of cell population proliferation / chromatin binding / chromatin / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / protein homodimerization activity / DNA binding / : / nucleoplasm / zinc ion binding / nucleus
Similarity search - Function
Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / Histone, subunit A / Histone, subunit A / DHS-like NAD/FAD-binding domain superfamily / : / Histone H2A conserved site ...Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / Histone, subunit A / Histone, subunit A / DHS-like NAD/FAD-binding domain superfamily / : / Histone H2A conserved site / Histone H2A signature. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 domain / Histone-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / DNA (> 100) / Histone H2B / Histone H2A type 1 / Histone H4 / Histone H3.2 / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog)
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.94 Å
AuthorsSmirnova, E. / Bignon, E. / Schultz, P. / Papai, G. / Ben-Shem, A.
Funding support France, 1items
OrganizationGrant numberCountry
Other private France
Citation
Journal: Elife / Year: 2024
Title: Binding to nucleosome poises human SIRT6 for histone H3 deacetylation.
Authors: Ekaterina Smirnova / Emmanuelle Bignon / Patrick Schultz / Gabor Papai / Adam Ben Shem /
Abstract: Sirtuin 6 (SIRT6) is an NAD-dependent histone H3 deacetylase that is prominently found associated with chromatin, attenuates transcriptionally active promoters and regulates DNA repair, metabolic ...Sirtuin 6 (SIRT6) is an NAD-dependent histone H3 deacetylase that is prominently found associated with chromatin, attenuates transcriptionally active promoters and regulates DNA repair, metabolic homeostasis and lifespan. Unlike other sirtuins, it has low affinity to free histone tails but demonstrates strong binding to nucleosomes. It is poorly understood how SIRT6 docking on nucleosomes stimulates its histone deacetylation activity. Here, we present the structure of human SIRT6 bound to a nucleosome determined by cryogenic electron microscopy. The zinc finger domain of SIRT6 associates tightly with the acidic patch of the nucleosome through multiple arginine anchors. The Rossmann fold domain binds to the terminus of the looser DNA half of the nucleosome, detaching two turns of the DNA from the histone octamer and placing the NAD binding pocket close to the DNA exit site. This domain shows flexibility with respect to the fixed zinc finger and moves with, but also relative to, the unwrapped DNA terminus. We apply molecular dynamics simulations of the histone tails in the nucleosome to show that in this mode of interaction, the active site of SIRT6 is perfectly poised to catalyze deacetylation of the H3 histone tail and that the partial unwrapping of the DNA allows even lysines close to the H3 core to reach the enzyme.
#1: Journal: Elife / Year: 2023
Title: Binding to nucleosome poises SIRT6 for histone H3 de-acetylation
Authors: Smirnova, E. / Bignon, E. / Schultz, P. / Papai, G. / Ben-Shem, A.
History
DepositionMar 13, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 9, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author / em_3d_fitting_list
Item: _em_3d_fitting_list.initial_refinement_model_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Histone H3.2
B: Histone H4
C: Histone H2A type 1
D: Histone H2B
E: Histone H3.2
F: Histone H4
G: Histone H2A type 1
H: Histone H2B
I: DNA (145-MER)
J: DNA (145-MER)
L: NAD-dependent protein deacylase sirtuin-6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,53512
Polymers238,46911
Non-polymers651
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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Protein , 5 types, 9 molecules AEBFCGDHL

#1: Protein Histone H3.2


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P84233
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P62799
#3: Protein Histone H2A type 1


Mass: 14093.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P06897
#4: Protein Histone H2B


Mass: 13979.291 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: LOC108704303 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8J0U496
#7: Protein NAD-dependent protein deacylase sirtuin-6 / NAD-dependent protein deacetylase sirtuin-6 / Protein mono-ADP-ribosyltransferase sirtuin-6 / ...NAD-dependent protein deacetylase sirtuin-6 / Protein mono-ADP-ribosyltransferase sirtuin-6 / Regulatory protein SIR2 homolog 6 / hSIRT6 / SIR2-like protein 6


Mass: 39180.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT6, SIR2L6 / Production host: Escherichia coli (E. coli)
References: UniProt: Q8N6T7, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups, protein acetyllysine N-acetyltransferase, Transferases; Glycosyltransferases; Pentosyltransferases

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (145-MER)


Mass: 44520.383 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli)
#6: DNA chain DNA (145-MER)


Mass: 44991.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli)

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Non-polymers , 1 types, 1 molecules

#8: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

Component
IDNameTypeEntity IDParent-IDSource
1Human Sirtuin 6 in complex with the nucleosomeCOMPLEX#1-#70RECOMBINANT
2SIRT6COMPLEX#71RECOMBINANT
Molecular weight
IDEntity assembly-IDExperimental value
11NO
22
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
21Xenopus laevis (African clawed frog)8355
32Homo sapiens (human)9606
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
21Escherichia coli (E. coli)562
32Escherichia coli (E. coli)562
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER/RHODIUM / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R3.5/1
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
EM imaging

Accelerating voltage: 300 kV / C2 aperture diameter: 50 µm / Cryogen: NITROGEN / Electron source: FIELD EMISSION GUN / Illumination mode: FLOOD BEAM / Model: TFS KRIOS / Mode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Specimen-ID: 1

IDAlignment procedureCs (mm)Nominal magnification (X)
1COMA FREE2.7270000
2ZEMLIN TABLEAU0.01180000
Image recording
IDImaging-IDElectron dose (e/Å2)Film or detector model
1150FEI FALCON IV (4k x 4k)
2255GATAN K3 (6k x 4k)
EM imaging optics
Energyfilter nameIDImaging-IDEnergyfilter slit width (eV)
TFS Selectris X1110
GIF Quantum LS2220

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Processing

EM software
IDNameCategoryImaging-ID
1crYOLOparticle selection
3EPUimage acquisition1
5cryoSPARCCTF correction
8UCSF Chimeramodel fitting
11cryoSPARCinitial Euler assignment
13cryoSPARCfinal Euler assignment
15RELIONclassification
17cryoSPARC3D reconstruction
19PHENIXmodel refinement
20ISOLDEmodel refinement
21SerialEMimage acquisition2
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 2033169
3D reconstructionResolution: 2.94 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 439796 / Algorithm: BACK PROJECTION / Symmetry type: POINT
Atomic model building
IDPDB-ID 3D fitting-IDAccession codeInitial refinement model-IDSource nameType
13LZ0

3lz0

13LZ01PDBexperimental model
25X16

5x16

15X162PDBexperimental model

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