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- EMDB-29735: Structure of nucleosome-bound Sirtuin 6 deacetylase -

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Basic information

Entry
Database: EMDB / ID: EMD-29735
TitleStructure of nucleosome-bound Sirtuin 6 deacetylase
Map dataMain map from cisTEM, aligned to the common point of reference with the PDB and cryoSPARC map
Sample
  • Complex: Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
    • Protein or peptide: NAD-dependent protein deacylase sirtuin-6
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA strand 1
    • DNA: DNA strand 2
KeywordsNucleosome / Sirt6 / aging / DNA damage / repair / deacetylation / diacylation / apo / chromatin / heterochromatin / GENE REGULATION / TRANSFERASE-DNA complex
Function / homology
Function and homology information


NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity ...NAD-dependent histone H3K56 deacetylase activity / NAD-dependent histone H3K18 deacetylase activity / NAD-dependent histone H3K9 deacetylase activity / protein delipidation / ketone biosynthetic process / NAD+-protein-lysine ADP-ribosyltransferase activity / regulation of lipid catabolic process / NAD-dependent protein demyristoylase activity / NAD-dependent protein depalmitoylase activity / NAD+-protein-arginine ADP-ribosyltransferase activity / positive regulation of protein localization to chromatin / chromosome, subtelomeric region / DNA damage sensor activity / positive regulation of stem cell differentiation / positive regulation of blood vessel branching / NAD-dependent protein lysine deacetylase activity / retrotransposon silencing / protein acetyllysine N-acetyltransferase / cardiac muscle cell differentiation / positive regulation of chondrocyte proliferation / pericentric heterochromatin formation / positive regulation of telomere maintenance / NAD-dependent histone deacetylase activity / protein deacetylation / negative regulation of glucose import / protein localization to site of double-strand break / TORC2 complex binding / negative regulation of glycolytic process / lncRNA binding / negative regulation of protein localization to chromatin / DNA repair-dependent chromatin remodeling / positive regulation of double-strand break repair / positive regulation of vascular endothelial cell proliferation / negative regulation of protein import into nucleus / regulation of double-strand break repair via homologous recombination / positive regulation of fat cell differentiation / negative regulation of gene expression, epigenetic / positive regulation of stem cell population maintenance / regulation of protein secretion / positive regulation of stem cell proliferation / negative regulation of transcription elongation by RNA polymerase II / NAD+-protein ADP-ribosyltransferase activity / negative regulation of cellular senescence / site of DNA damage / protein localization to CENP-A containing chromatin / CENP-A containing nucleosome / regulation of lipid metabolic process / NAD+-protein poly-ADP-ribosyltransferase activity / Transferases; Glycosyltransferases; Pentosyltransferases / NAD+ binding / negative regulation of tumor necrosis factor-mediated signaling pathway / subtelomeric heterochromatin formation / Replacement of protamines by nucleosomes in the male pronucleus / nucleosome binding / Packaging Of Telomere Ends / regulation of protein localization to plasma membrane / negative regulation of gluconeogenesis / pericentric heterochromatin / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / Deposition of new CENPA-containing nucleosomes at the centromere / response to UV / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Meiotic synapsis / Inhibition of DNA recombination at telomere / nucleosomal DNA binding / RNA Polymerase I Promoter Opening / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Assembly of the ORC complex at the origin of replication / nucleotidyltransferase activity / DNA methylation / HCMV Late Events / Condensation of Prophase Chromosomes / SIRT1 negatively regulates rRNA expression / Chromatin modifications during the maternal to zygotic transition (MZT) / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / positive regulation of protein export from nucleus / Defective pyroptosis / Meiotic recombination / innate immune response in mucosa / DNA Damage/Telomere Stress Induced Senescence / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / determination of adult lifespan / regulation of circadian rhythm / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Transcriptional regulation of granulopoiesis / Formation of the beta-catenin:TCF transactivating complex / HCMV Early Events / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / G2/M DNA damage checkpoint / circadian regulation of gene expression / NoRC negatively regulates rRNA expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / protein destabilization / B-WICH complex positively regulates rRNA expression
Similarity search - Function
: / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 ...: / Sirtuin family / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H2A / Histone 2A / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H3 / Histone H2A type 1-B/E / Histone H2B type 1-J / Histone H4 / NAD-dependent protein deacylase sirtuin-6
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsChio US / Rechiche O / Bryll AR / Zhu J / Feldman JL / Peterson CL / Tan S / Armache J-P
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F32GM137463 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127034 United States
National Institutes of Health/National Institute of Biomedical Imaging and Bioengineering (NIH/NIBIB)T32BM107000 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM127034 United States
CitationJournal: Sci Adv / Year: 2023
Title: Cryo-EM structure of the human Sirtuin 6-nucleosome complex.
Authors: Un Seng Chio / Othman Rechiche / Alysia R Bryll / Jiang Zhu / Erik M Leith / Jessica L Feldman / Craig L Peterson / Song Tan / Jean-Paul Armache /
Abstract: Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups ...Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.
History
DepositionFeb 11, 2023-
Header (metadata) releaseApr 26, 2023-
Map releaseApr 26, 2023-
UpdateJun 19, 2024-
Current statusJun 19, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_29735.png

Downloads & links

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Map

FileDownload / File: emd_29735.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMain map from cisTEM, aligned to the common point of reference with the PDB and cryoSPARC map
Voxel sizeX=Y=Z: 1.08 Å
Density
Contour LevelBy AUTHOR: 2.0
Minimum - Maximum-6.5175138 - 15.483361
Average (Standard dev.)0.0013880634 (±0.39455706)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 324.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Main map from cisTEM in original position

Fileemd_29735_additional_1.map
AnnotationMain map from cisTEM in original position
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened main map from cisTEM, aligned to the...

Fileemd_29735_additional_2.map
AnnotationSharpened main map from cisTEM, aligned to the common point of reference with the PDB and cryoSPARC map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened and aligned main map from cryoSPARC

Fileemd_29735_additional_3.map
AnnotationSharpened and aligned main map from cryoSPARC
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 1 from cisTEM

Fileemd_29735_half_map_1.map
AnnotationHalf map 1 from cisTEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map 2 from cisTEM

Fileemd_29735_half_map_2.map
AnnotationHalf map 2 from cisTEM
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601...

EntireName: Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
Components
  • Complex: Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
    • Protein or peptide: NAD-dependent protein deacylase sirtuin-6
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 1-B/E
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA strand 1
    • DNA: DNA strand 2

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Supramolecule #1: Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601...

SupramoleculeName: Sirt6 deacetylase bound to a nucleosome assembled with 172-bp 601 Widom DNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 300 kDa/nm

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Macromolecule #1: NAD-dependent protein deacylase sirtuin-6

MacromoleculeName: NAD-dependent protein deacylase sirtuin-6 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
EC number: Transferases; Acyltransferases; Transferring groups other than aminoacyl groups
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 39.708508 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GSMSVNYAAG LSPYADKGKC GLPEIFDPPE ELERKVWELA RLVWQSSNVV FHTGAGISTA SGIPDFRGPH GVWTMEERGL APKFDTTFE SARPTQTHMA LVQLERVGLL RFLVSQNVDG LHVRSGFPRD KLAELHGNMF VEECAKCKTQ YVRDTVVGTM G LKATGRLC ...String:
GSMSVNYAAG LSPYADKGKC GLPEIFDPPE ELERKVWELA RLVWQSSNVV FHTGAGISTA SGIPDFRGPH GVWTMEERGL APKFDTTFE SARPTQTHMA LVQLERVGLL RFLVSQNVDG LHVRSGFPRD KLAELHGNMF VEECAKCKTQ YVRDTVVGTM G LKATGRLC TVAKARGLRA CRGELRDTIL DWEDSLPDRD LALADEASRN ADLSITLGTS LQIRPSGNLP LATKRRGGRL VI VNLQPTK HDRHADLRIH GYVDEVMTRL MKHLGLEIPA WDGPRVLERA LPPLPRPPTP KLEPKEESPT RINGSIPAGP KQE PCAQHN GSEPASPKRE RPTSPAPHRP PKRVKAKAVP SKLN

UniProtKB: NAD-dependent protein deacylase sirtuin-6

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Macromolecule #2: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.004579 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TKQTARKSTG GKAPRKQLAT KAARKSAPAT GGVKKPHRYR PGTVALREIR RYQKSTELLI RKLPFQRLVR EIAQDFKTDL RFQSSAVMA LQEASEAYLV ALFEDTNLCA IHAKRVTIMP KDIQLARRIR GER

UniProtKB: Histone H3

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Macromolecule #3: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 9.704396 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
HRKVLRDNIQ GITKPAIRRL ARRGGVKRIS GLIYEETRGV LKVFLENVIR DAVTYTEHAK RKTVTAMDVV YALKRQGRTL YGFGG

UniProtKB: Histone H4

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Macromolecule #4: Histone H2A type 1-B/E

MacromoleculeName: Histone H2A type 1-B/E / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 14.034355 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKTRSSR AGLQFPVGRV HRLLRKGNYS ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGR VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 1-B/E

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Macromolecule #5: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 5 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.804045 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
PEPAKSAPAP KKGSKKAVTK AQKKDGKKRK RSRKESYSIY VYKVLKQVHP DTGISSKAMG IMNSFVNDIF ERIAGEASRL AHYNKRSTI TSREIQTAVR LLLPGELAKH AVSEGTKAVT KYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #6: DNA strand 1

MacromoleculeName: DNA strand 1 / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.541637 KDa
SequenceString: (DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(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) ...String:
(DT)(DG)(DC)(DA)(DC)(DA)(DG)(DG)(DA)(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)(DC)(DG)(DA)(DT)

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Macromolecule #7: DNA strand 2

MacromoleculeName: DNA strand 2 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 46.061348 KDa
SequenceString: (DA)(DT)(DC)(DG)(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) ...String:
(DA)(DT)(DC)(DG)(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)(DT)(DC) (DC)(DT)(DG)(DT)(DG)(DC)(DA)

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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

Concentration1.2 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
60.0 mMKClPotassium chloride
12.5 mMHEPES2-[4-(2-Hydroxyethyl)piperazin-1-yl]ethane-1-sulfonic acid
1.0 mMDithiothreitol(2S,3S)-1,4-Bis(sulfanyl)butane-2,3-diol
1.5 %GlycerolPropane-1,2,3-triol

Details: 12.5 mM HEPES pH 7.5, 60 mM KCl, 1.5% glycerol, 1 mM DTT
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 1 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 10 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.2 kPa
Details: Glass slides were wrapped with fresh parafilm. Tweezers were washed with ethanol, dried, and then used to pick grids from a grid box. Grids were carefully examined and placed on the parafilm- ...Details: Glass slides were wrapped with fresh parafilm. Tweezers were washed with ethanol, dried, and then used to pick grids from a grid box. Grids were carefully examined and placed on the parafilm-covered slides. These slides were then placed into the PelCO easyGLOW glow discharger, and treated there.
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
DetailsSIRT6 deacetylase bound to asymmetrical nucleosome with 172 DNA base-pairs

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 64.0 K / Max: 75.0 K
Specialist opticsPhase plate: OTHER / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Number grids imaged: 2 / Number real images: 11872 / Average exposure time: 3.3 sec. / Average electron dose: 50.0 e/Å2
Details: Data was collected in Super Resolution mode, thus the image size is 11520 (width) x 8184 (height)
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Calibrated defocus max: 2.2 µm / Calibrated defocus min: 1.0 µm / Calibrated magnification: 81000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 81000
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

Particle selectionNumber selected: 12821862 / Details: Particles were selected using Blob Picker
Startup modelType of model: INSILICO MODEL
Details: Using Ab initio option, five starting models were selected; the most relevant was assessed based on its similarity to known nucleosome structures
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 3.32) / Number images used: 71603
Initial angle assignmentType: PROJECTION MATCHING / Details: Using cryoSPARC Homogeneous Refinement
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cryoSPARC (ver. 3.32) / Details: Using cryoSPARC NonUniform Refinement
Final 3D classificationNumber classes: 1 / Software - Name: cryoSPARC (ver. 3.32)

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Atomic model buiding 1

Initial model
PDB IDChain

3lz0

source_name: PDB, initial_model_type: experimental model

3pki

source_name: PDB, initial_model_type: experimental model

7cl0

source_name: PDB, initial_model_type: experimental model
DetailsUCSF Chimera was used for manual fitting of the models; It was then used for optimizing the fit by using option Fit in Map. Then Coot was used to analyze the fits, build and adjust the models into the existing densities, and refine parts of the model. Once the model has been built, validated and adjusted, we used phenix.real_space_refine to fix and improve the fit into the densities
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 79
Output model

PDB-8g57:
Structure of nucleosome-bound Sirtuin 6 deacetylase

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