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- PDB-6px1: Set2 bound to nucleosome -

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Basic information

Entry
Database: PDB / ID: 6px1
TitleSet2 bound to nucleosome
Components
  • (DNA (149-MER)) x 2
  • Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Ubiquitin-60S ribosomal protein L40,Histone H2A
KeywordsGENE REGULATION / Set2 / nucleosome / chromatin / KMT
Function / homology
Function and homology information


ribosomal large subunit export from nucleus / DNA-templated transcription, initiation / modification-dependent protein catabolic process / nucleosome / protein tag / cytoplasmic translation / ribosome biogenesis / cytosolic large ribosomal subunit / ribosomal large subunit assembly / structural constituent of ribosome ...ribosomal large subunit export from nucleus / DNA-templated transcription, initiation / modification-dependent protein catabolic process / nucleosome / protein tag / cytoplasmic translation / ribosome biogenesis / cytosolic large ribosomal subunit / ribosomal large subunit assembly / structural constituent of ribosome / protein ubiquitination / protein heterodimerization activity / ubiquitin protein ligase binding / mitochondrion / DNA binding / nucleus / cytoplasm
Histone H2A/H2B/H3 / Ubiquitin domain / Histone H4 / Ubiquitin-like domain / Histone H2B / Histone H3/CENP-A / TATA box binding protein associated factor (TAF) / Histone-fold / Histone H4, conserved site / Ubiquitin conserved site ...Histone H2A/H2B/H3 / Ubiquitin domain / Histone H4 / Ubiquitin-like domain / Histone H2B / Histone H3/CENP-A / TATA box binding protein associated factor (TAF) / Histone-fold / Histone H4, conserved site / Ubiquitin conserved site / Ubiquitin-like domain superfamily / Histone H2A / Histone H2A, C-terminal domain / Histone H2A conserved site / CENP-T/Histone H4, histone fold / Ribosomal protein L40e superfamily / Core histone H2A/H2B/H3/H4 / Centromere kinetochore component CENP-T histone fold / C-terminus of histone H2A / Ubiquitin family / Ribosomal protein L40e / Histone, subunit A / Histone, subunit A / Orthogonal Bundle / Mainly Alpha
Histone H3 / Histone H3.3C / Ubiquitin-60S ribosomal protein L40 / Histone H4 / Histone H2A / Histone H2B 1.1
Biological speciesXenopus laevis (African clawed frog)
Saccharomyces cerevisiae (baker's yeast)
synthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsHalic, M. / Bilokapic, S.
CitationJournal: Nat Commun / Year: 2019
Title: Nucleosome and ubiquitin position Set2 to methylate H3K36.
Authors: Silvija Bilokapic / Mario Halic /
Abstract: Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes ...Histone H3 lysine 36 methylation (H3K36me) is a conserved histone modification deposited by the Set2 methyltransferases. Recent findings show that over-expression or mutation of Set2 enzymes promotes cancer progression, however, mechanisms of H3K36me are poorly understood. Set2 enzymes show spurious activity on histones and histone tails, and it is unknown how they obtain specificity to methylate H3K36 on the nucleosome. In this study, we present 3.8 Å cryo-EM structure of Set2 bound to the mimic of H2B ubiquitinated nucleosome. Our structure shows that Set2 makes extensive interactions with the H3 αN, the H3 tail, the H2A C-terminal tail and stabilizes DNA in the unwrapped conformation, which positions Set2 to specifically methylate H3K36. Moreover, we show that ubiquitin contributes to Set2 positioning on the nucleosome and stimulates the methyltransferase activity. Notably, our structure uncovers interfaces that can be targeted by small molecules for development of future cancer therapies.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJul 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 28, 2019Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name

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Structure visualization

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  • Deposited structure unit
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Histone H3
B: Histone H4
C: Ubiquitin-60S ribosomal protein L40,Histone H2A
D: Histone H2B 1.1
E: Histone H3
F: Histone H4
G: Ubiquitin-60S ribosomal protein L40,Histone H2A
H: Histone H2B 1.1
I: DNA (149-MER)
J: DNA (149-MER)


Theoretical massNumber of molelcules
Total (without water)221,05210
Polymers221,05210
Non-polymers00
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area57220 Å2
ΔGint-395 kcal/mol
Surface area71470 Å2

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Components

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Protein , 4 types, 8 molecules AEBFCGDH

#1: Protein Histone H3 /


Mass: 15437.144 Da / Num. of mol.: 2 / Mutation: K36M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Gene: XELAEV_18002543mg / Production host: Escherichia coli (E. coli) / References: UniProt: A0A310TTQ1, UniProt: P02302*PLUS
#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 Ubiquitin-60S ribosomal protein L40,Histone H2A


Mass: 24045.436 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast), (gene. exp.) Xenopus laevis (African clawed frog)
Strain: ATCC 204508 / S288c
Gene: RPL40B, UBI2, YKR094C, hist1h2aj, LOC494591, XELAEV_18003602mg
Production host: Escherichia coli (E. coli) / References: UniProt: P0CH09, UniProt: Q6AZJ8
#4: Protein Histone H2B 1.1 / H2B1.1


Mass: 13655.948 Da / Num. of mol.: 2 / Mutation: S29T
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xenopus laevis (African clawed frog) / Production host: Escherichia coli (E. coli) / References: UniProt: P02281

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DNA chain , 2 types, 2 molecules IJ

#5: DNA chain DNA (149-MER)


Mass: 45764.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: DNA chain DNA (149-MER)


Mass: 46222.434 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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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-IDSourceDetails
1NucleosomeCOMPLEX#1-#60MULTIPLE SOURCES
2Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1COMPLEX#1-#41RECOMBINANThistone-lysine N-methyltransferase and ubiquitin not visible in this EM map
3DNACOMPLEX#5-#61RECOMBINANTDNA was obtained by PCR reaction synthetic source
Molecular weightValue: 0.2 MDa / Experimental value: NO
Source (natural)
IDEntity assembly-IDOrganismNcbi tax-ID
12Xenopus laevis (African clawed frog)8355
23synthetic construct (others)32630
Source (recombinant)
IDEntity assembly-IDOrganismNcbi tax-ID
12Escherichia coli (E. coli)562
23synthetic construct (others)32630
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 75 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.16_3546: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 77000 / Symmetry type: POINT
Refine LS restraints
Refinement-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00612740
ELECTRON MICROSCOPYf_angle_d0.85918447
ELECTRON MICROSCOPYf_dihedral_angle_d26.5686668
ELECTRON MICROSCOPYf_chiral_restr0.052098
ELECTRON MICROSCOPYf_plane_restr0.0081330

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