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- PDB-9gmr: SIRT7-H3K36MTUnucleosome complex -

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Basic information

Entry
Database: PDB / ID: 9gmr
TitleSIRT7-H3K36MTUnucleosome complex
Components
  • (DNA (149-MER)) x 2
  • Histone H2A type 2-A
  • Histone H2B type 1-J
  • Histone H3.2
  • Histone H4
  • NAD-dependent protein deacetylase sirtuin-7
KeywordsDNA / nucleosome complex
Function / homology
Function and homology information


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 / homologous chromosome pairing at meiosis / R-loop processing / regulation of protein export from nucleus ...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 / homologous chromosome pairing at meiosis / R-loop processing / regulation of protein export from nucleus / positive regulation of transcription of nucleolar large rRNA by RNA polymerase I / protein methyltransferase activity / transposable element silencing / protein acetyllysine N-acetyltransferase / NAD-dependent protein lysine deacetylase activity / regulation of mitochondrion organization / protein deacetylation / positive regulation of rRNA processing / rRNA transcription / negative regulation of gene expression, epigenetic / ChAHP complex assembly / positive regulation of transcription by RNA polymerase I / DNA repair-dependent chromatin remodeling / NAD+ binding / FXIIa activates plasma kallikrein-kinin system / negative regulation of tumor necrosis factor-mediated signaling pathway / Interaction of NuRD complexes with transcription factors / CHD6, CHD7, CHD8, CHD9 subfamily / NuRD complex assembly / CHD1 and CHD2 subfamily / positive regulation of gluconeogenesis / negative regulation of megakaryocyte differentiation / protein localization to CENP-A containing chromatin / Chromatin modifying enzymes / Replacement of protamines by nucleosomes in the male pronucleus / negative regulation of protein ubiquitination / Packaging Of Telomere Ends / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / Recognition and association of DNA glycosylase with site containing an affected purine / Cleavage of the damaged purine / regulation of DNA repair / telomere organization / Interleukin-7 signaling / 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 / transcription initiation-coupled chromatin remodeling / RNA Polymerase I Promoter Opening / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Inhibition of DNA recombination at telomere / 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 / Meiotic synapsis / DNA methylation / Condensation of Prophase Chromosomes / Chromatin modifications during the maternal to zygotic transition (MZT) / SIRT1 negatively regulates rRNA expression / HCMV Late Events / 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 / Transcriptional regulation by small RNAs / lipopolysaccharide binding / Regulation of endogenous retroelements by Piwi-interacting RNAs (piRNAs) / RNA Polymerase I Promoter Escape / Nonhomologous End-Joining (NHEJ) / HDMs demethylate histones / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Negative Regulation of CDH1 Gene Transcription / NoRC negatively regulates rRNA expression / PKMTs methylate histone lysines / G2/M DNA damage checkpoint / Formation of the beta-catenin:TCF transactivating complex / B-WICH complex positively regulates rRNA expression / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / Pre-NOTCH Transcription and Translation / Activation of anterior HOX genes in hindbrain development during early embryogenesis / osteoblast differentiation / Transcriptional regulation of granulopoiesis / nucleosomal DNA binding / RMTs methylate histone arginines / Metalloprotease DUBs / HCMV Early Events / innate immune response in mucosa / structural constituent of chromatin / nucleosome / Regulation of PD-L1(CD274) transcription / UCH proteinases / nucleosome assembly / site of double-strand break / HATs acetylate histones / E3 ubiquitin ligases ubiquitinate target proteins / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Factors involved in megakaryocyte development and platelet production / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis
Similarity search - Function
Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / : / DHS-like NAD/FAD-binding domain superfamily / : / Histone H2A conserved site / Histone H2A signature. ...Sirtuin family / : / Sir2 family / Sirtuin family, catalytic core domain / Sirtuin catalytic domain profile. / : / 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
Similarity search - Domain/homology
: / DNA / DNA (> 10) / DNA (> 100) / 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)
MethodELECTRON MICROSCOPY / single 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, 4items
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, 2024Deposition site: PDBE / Processing site: PDBE
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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 2-A
D: Histone H2B type 1-J
E: Histone H3.2
F: Histone H4
G: Histone H2A type 2-A
H: Histone H2B type 1-J
I: DNA (149-MER)
J: DNA (149-MER)
K: NAD-dependent protein deacetylase sirtuin-7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,19313
Polymers246,45411
Non-polymers7392
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area58100 Å2
ΔGint-402 kcal/mol
Surface area95420 Å2

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Components

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Protein , 5 types, 9 molecules AEBFCGDHK

#1: Protein Histone H3.2 / H3-clustered histone 13 / H3-clustered histone 14 / H3-clustered histone 15 / Histone H3/m / Histone H3/o


Mass: 15421.101 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H3C15, HIST2H3A, H3C14, H3F2, H3FM, HIST2H3C, H3C13, HIST2H3D
Production host: Escherichia coli (E. coli) / References: UniProt: Q71DI3
#2: Protein Histone H4


Mass: 11394.426 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, ...Gene: H4C1, H4/A, H4FA, HIST1H4A, H4C2, H4/I, H4FI, HIST1H4B, H4C3, H4/G, H4FG, HIST1H4C, H4C4, H4/B, H4FB, HIST1H4D, H4C5, H4/J, H4FJ, HIST1H4E, H4C6, H4/C, H4FC, HIST1H4F, H4C8, H4/H, H4FH, HIST1H4H, H4C9, H4/M, H4FM, HIST1H4I, H4C11, H4/E, H4FE, HIST1H4J, H4C12, H4/D, H4FD, HIST1H4K, H4C13, H4/K, H4FK, HIST1H4L, H4C14, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4C15, H4/O, H4FO, HIST2H4B, H4C16, H4-16, HIST4H4
Production host: Escherichia coli (E. coli) / References: UniProt: P62805
#3: Protein Histone H2A type 2-A / Histone H2A.2 / Histone H2A/o


Mass: 13994.354 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: HIST2H2AA3, H2AFO, HIST2H2AA, HIST2H2AA4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q6FI13
#4: Protein Histone H2B type 1-J / Histone H2B.1 / Histone H2B.r / H2B/r


Mass: 13907.226 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: H2BC11, H2BFR, HIST1H2BJ / Production host: Escherichia coli (E. coli) / References: UniProt: P06899
#7: Protein NAD-dependent protein deacetylase sirtuin-7 / NAD-dependent protein deacylase sirtuin-7 / Regulatory protein SIR2 homolog 7 / SIR2-like protein 7


Mass: 45035.590 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SIRT7, SIR2L7 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9NRC8, protein acetyllysine N-acetyltransferase, Transferases; Acyltransferases; Transferring groups other than aminoacyl groups

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (149-MER)


Mass: 45701.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#6: DNA chain DNA (149-MER)


Mass: 46283.469 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 2 types, 2 molecules

#8: Chemical ChemComp-A1IY0 / [[(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


Mass: 673.528 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H33N7O13P2S / Feature type: SUBJECT OF INVESTIGATION
#9: 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
Has protein modificationY

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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

ComponentName: K36 structure / Type: COMPLEX / Entity ID: #1-#7 / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2500 nm / Nominal defocus min: 1200 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)
EM imaging opticsEnergyfilter name: TFS Selectris X

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 337476 / Symmetry type: POINT
Atomic model buildingProtocol: AB INITIO MODEL / Space: REAL
RefinementHighest resolution: 2.8 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00415634
ELECTRON MICROSCOPYf_angle_d0.53822393
ELECTRON MICROSCOPYf_dihedral_angle_d29.5734216
ELECTRON MICROSCOPYf_chiral_restr0.0342537
ELECTRON MICROSCOPYf_plane_restr0.0041807

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