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- EMDB-18497: Human Sirtuin 6 in complex with nucleosome - structure showing H2... -

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Basic information

Entry
Database: EMDB / ID: EMD-18497
TitleHuman Sirtuin 6 in complex with nucleosome - structure showing H2A tail path
Map data
Sample
  • Complex: Human Sirtuin 6 in complex with nucleosome
    • Protein or peptide: Sirtuin 6
KeywordsHistone deacetylase / Sirtuin / nucleosome / TRANSCRIPTION
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.78 Å
AuthorsSmirnova E / Bignon E / Schultz P / Papai G / Ben-Shem A
Funding support France, 1 items
OrganizationGrant numberCountry
La ligue contre le cancer France
CitationJournal: 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.
History
DepositionSep 22, 2023-
Header (metadata) releaseMar 6, 2024-
Map releaseMar 6, 2024-
UpdateMar 13, 2024-
Current statusMar 13, 2024Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_18497.png

Downloads & links

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Map

FileDownload / File: emd_18497.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 0.862 Å
Density
Contour LevelBy AUTHOR: 0.0731
Minimum - Maximum-0.19939809 - 0.39458537
Average (Standard dev.)0.002577472 (±0.01745204)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 220.672 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_18497_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_18497_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Human Sirtuin 6 in complex with nucleosome

EntireName: Human Sirtuin 6 in complex with nucleosome
Components
  • Complex: Human Sirtuin 6 in complex with nucleosome
    • Protein or peptide: Sirtuin 6

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Supramolecule #1: Human Sirtuin 6 in complex with nucleosome

SupramoleculeName: Human Sirtuin 6 in complex with nucleosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: Sirtuin 6

MacromoleculeName: Sirtuin 6 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSVNYAAGLS PYADKGKCGL PEIFDPPEEL ERKVWELARL VWQSSSVVFH TGAGISTASG IPDFRGPHG VWTMEERGLA PKFDTTFESA RPTQTHMALV QLERVGLLRF LVSQNVDGLH V RSGFPRDK LAELHGNMFV EECAKCKTQY VRDTVVGTMG LKATGRLCTV ...String:
MSVNYAAGLS PYADKGKCGL PEIFDPPEEL ERKVWELARL VWQSSSVVFH TGAGISTASG IPDFRGPHG VWTMEERGLA PKFDTTFESA RPTQTHMALV QLERVGLLRF LVSQNVDGLH V RSGFPRDK LAELHGNMFV EECAKCKTQY VRDTVVGTMG LKATGRLCTV AKARGLRACR GE LRDTILD WEDSLPDRDL ALADEASRNA DLSITLGTSL QIRPSGNLPL ATKRRGGRLV IVN LQPTKH DRHADLRIHG YVDEVMTRLM KHLGLEIPAW DGPRVLERAL PPLPRPPTPK LEPK EESPT RINGSIPAGP KQEPCAQHNG SEPASPKRER PTSPAPHRPP KRVKAKAVPS

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 20 mM Hepes pH 7.5, 2% glycerol v/v, 0.5 mM TCEP and 150 mM NaCl
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: PLASMA CLEANING / Pretreatment - Time: 90 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 279 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 48.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.2 µm / Nominal defocus min: 1.1 µm
Sample stageSpecimen 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

Startup modelType of model: OTHER / Details: Ab-initio in cryoSPARC
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.78 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 97164
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC

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