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- EMDB-51453: SIRT7-H3K36MTUnucleosome complex -

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Basic information

Entry
Database: EMDB / ID: EMD-51453
TitleSIRT7-H3K36MTUnucleosome complex
Map data
Sample
  • Complex: K36 structure
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-A
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (149-MER)
    • DNA: DNA (149-MER)
    • Protein or peptide: NAD-dependent protein deacetylase sirtuin-7
  • Ligand: [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
  • Ligand: ZINC ION
Keywordsnucleosome complex / DNA
Function / homology
Function and homology information


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 / protein-succinyllysine desuccinylase activity / R-loop processing / homologous chromosome pairing at meiosis / protein methyltransferase activity ...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 / protein-succinyllysine desuccinylase activity / R-loop processing / homologous chromosome pairing at meiosis / protein methyltransferase activity / NAD-dependent protein lysine deacetylase activity / transposable element silencing / protein acetyllysine N-acetyltransferase / histone H3K14 deacetylase activity, NAD-dependent / histone H3K9 deacetylase activity, NAD-dependent / histone H4K16 deacetylase activity, NAD-dependent / histone H3K18 deacetylase activity, NAD-dependent / histone H3K56 deacetylase activity, NAD-dependent / histone H3K4 deacetylase activity, NAD-dependent / positive regulation of rRNA processing / protein deacetylation / regulation of protein export from nucleus / 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 / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / regulation of DNA repair / 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 / Recognition and association of DNA glycosylase with site containing an affected pyrimidine / Cleavage of the damaged pyrimidine / Deposition of new CENPA-containing nucleosomes at the centromere / negative regulation of protein ubiquitination / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / positive regulation of gluconeogenesis / telomere organization / Inhibition of DNA recombination at telomere / Meiotic synapsis / Interleukin-7 signaling / RNA Polymerase I Promoter Opening / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Assembly of the ORC complex at the origin of replication / transcription initiation-coupled chromatin remodeling / Regulation of endogenous retroelements by the Human Silencing Hub (HUSH) complex / innate immune response in mucosa / SUMOylation of chromatin organization proteins / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / HCMV Late Events / SIRT1 negatively regulates rRNA expression / ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression / PRC2 methylates histones and DNA / Regulation of endogenous retroelements by KRAB-ZFP proteins / Defective pyroptosis / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / HDACs deacetylate histones / Nonhomologous End-Joining (NHEJ) / RNA Polymerase I Promoter Escape / lipopolysaccharide binding / Transcriptional regulation by small RNAs / Formation of the beta-catenin:TCF transactivating complex / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / G2/M DNA damage checkpoint / HDMs demethylate histones / 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 / antibacterial humoral response / UCH proteinases / nucleosome / heterochromatin formation / E3 ubiquitin ligases ubiquitinate target proteins / nucleosome assembly / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / chromatin organization / 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
Similarity search - Function
Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / : / Histone H2B signature. / Histone H2B / Histone H2B ...Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / DHS-like NAD/FAD-binding domain superfamily / : / 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 / 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 / Histone-fold
Similarity search - Domain/homology
Histone H2B type 1-J / Histone H4 / Histone H2A type 2-A / Histone H3.2 / NAD-dependent protein deacetylase sirtuin-7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsMoreno-Yruela C / Ekundayo B / Foteva P / Calvino-Sanles E / Ni D / Stahlberg H / Fierz B
Funding support Switzerland, Denmark, Spain, 4 items
OrganizationGrant numberCountry
Swiss National Science Foundation#TMPFP2_217187 Switzerland
Independent Research Fund Denmark - Medical Sciences#2028.00011B Denmark
Swiss National Science FoundationIZLCZO_206089 Switzerland
La Caixa Foundation100010434 Spain
CitationJournal: Nat Commun / Year: 2025
Title: 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
DepositionAug 29, 2024-
Header (metadata) releaseJan 29, 2025-
Map releaseJan 29, 2025-
UpdateMar 12, 2025-
Current statusMar 12, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51453.png

Downloads & links

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Map

FileDownload / File: emd_51453.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å		0.83 Å/pix.
x 360 pix.
= 298.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0649
Minimum - Maximum-0.58121634 - 1.0233227
Average (Standard dev.)-0.0001187552 (±0.02442137)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 298.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_51453_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_51453_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : K36 structure

EntireName: K36 structure
Components
  • Complex: K36 structure
    • Protein or peptide: Histone H3.2
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A type 2-A
    • Protein or peptide: Histone H2B type 1-J
    • DNA: DNA (149-MER)
    • DNA: DNA (149-MER)
    • Protein or peptide: NAD-dependent protein deacetylase sirtuin-7
  • Ligand: [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
  • Ligand: ZINC ION

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Supramolecule #1: K36 structure

SupramoleculeName: K36 structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 15.421101 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MARTKQTARK STGGKAPRKQ LATKAARKSA PATGGVKKPH RYRPGTVCLR EIRRYQKSTE LLIRKLPFQR LVREIAQDFK TDLRFQSSA VMALQEASEA YLVGLFEDTN LAAIHAKRVT IMPKDIQLAR RIRGERA

UniProtKB: Histone H3.2

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 11.394426 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 2-A

MacromoleculeName: Histone H2A type 2-A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.994354 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKA RAKAKSRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY MAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAIRN DEELNKLLGK VTIAQGGVLP NIQAVLLPKK TESHHKAKGK

UniProtKB: Histone H2A type 2-A

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Macromolecule #4: Histone H2B type 1-J

MacromoleculeName: Histone H2B type 1-J / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 13.907226 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MPEPAKSAPA PKKGSKKAVT KAQKKDGKKR KKSRKESYSI YVYKVLKQVH PDTGISSKAM GIMNSFVNDI FERIAGEASR LAHYNKRST ITSREIQTAV RLLLPGELAK HAVSEGTKAV TKYTSAK

UniProtKB: Histone H2B type 1-J

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Macromolecule #7: NAD-dependent protein deacetylase sirtuin-7

MacromoleculeName: NAD-dependent protein deacetylase sirtuin-7 / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: protein acetyllysine N-acetyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.03559 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #5: DNA (149-MER)

MacromoleculeName: DNA (149-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 45.701125 KDa
SequenceString: (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)(DG)(DA) (DT)(DC)(DC) (DC)(DC)(DT)(DT)(DA)(DC)

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Macromolecule #6: DNA (149-MER)

MacromoleculeName: DNA (149-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 46.283469 KDa
SequenceString: (DG)(DT)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DC)(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) ...String:
(DG)(DT)(DA)(DA)(DG)(DG)(DG)(DG)(DA)(DT) (DC)(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)

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Macromolecule #8: [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxida...

MacromoleculeName: [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] ...Name: [[(2~{R},3~{a}~{R},5~{R},6~{R},6~{a}~{R})-2-(methylamino)-6-oxidanyl-2-(propylamino)-3~{a},5,6,6~{a}-tetrahydrofuro[2,3-d][1,3]oxathiol-5-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
type: ligand / ID: 8 / Number of copies: 1 / Formula: A1IY0
Molecular weightTheoretical: 673.528 Da

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Macromolecule #9: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 9 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 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 mg/mL
BufferpH: 8
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: TFS Selectris X
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 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 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 337476
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: PROJECTION MATCHING
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-9gmr:
SIRT7-H3K36MTUnucleosome complex

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