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- EMDB-20517: Set2 bound to nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-20517
TitleSet2 bound to nucleosome
Map data
SampleSet2 bound to ubiquitinated nucleosome
  • (Histone-lysine N- ...) x 2
  • DNA
  • Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1
  • Histone H3
  • Histone H4
  • Ubiquitin-60S ribosomal protein L40,Histone H2A
  • Histone H2B 1.1
  • (nucleic-acidNucleic acid) x 2
  • ligand
Function / homology
Function and homology information


[histone H3]-lysine36 N-trimethyltransferase / histone methyltransferase activity (H3-K36 specific) / : / Termination of translesion DNA synthesis / ribosomal large subunit export from nucleus / DNA-templated transcription, initiation / modification-dependent protein catabolic process / nucleosome / protein tag / cytosolic large ribosomal subunit ...[histone H3]-lysine36 N-trimethyltransferase / histone methyltransferase activity (H3-K36 specific) / : / Termination of translesion DNA synthesis / ribosomal large subunit export from nucleus / DNA-templated transcription, initiation / modification-dependent protein catabolic process / nucleosome / protein tag / cytosolic large ribosomal subunit / cytoplasmic translation / ribosome biogenesis / ribosomal large subunit assembly / chromosome / protein ubiquitination / structural constituent of ribosome / protein heterodimerization activity / regulation of transcription, DNA-templated / ubiquitin protein ligase binding / mitochondrion / DNA binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone-lysine N-methyltransferase, Set2, fungi / SRI (Set2 Rpb1 interacting) domain / Set2 Rpb1 interacting domain superfamily / Set2 Rpb1 interacting domain / SETD2/Set2, SET domain / AWS domain / associated with SET domains / AWS domain profile. / AWS domain ...Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Histone-lysine N-methyltransferase, Set2, fungi / SRI (Set2 Rpb1 interacting) domain / Set2 Rpb1 interacting domain superfamily / Set2 Rpb1 interacting domain / SETD2/Set2, SET domain / AWS domain / associated with SET domains / AWS domain profile. / AWS domain / TFIIS/LEDGF domain superfamily / Cysteine-rich motif following a subset of SET domains / Post-SET domain profile. / Post-SET domain / Ribosomal L40e family / Ribosomal_L40e / Ribosomal protein L40e / Ribosomal protein L40e superfamily / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / Domain with 2 conserved Trp (W) residues / SET domain / WW/rsp5/WWP domain profile. / WW domain / SET domain profile. / SET domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A signature. / Histone H2A conserved site / C-terminus of histone H2A / Histone H2A, C-terminal domain / Histone 2A / Histone H2A / Histone H4 signature. / Histone H4, conserved site / Histone H4 / Histone H4 / Centromere kinetochore component CENP-T histone fold / CENP-T/Histone H4, histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF) / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Core histone H2A/H2B/H3/H4 / Histone H2A/H2B/H3 / Ubiquitin conserved site / Ubiquitin domain signature. / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily
Similarity search - Domain/homology
Histone H3 / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Histone H2B 1.1 / Histone H3.3C / Ubiquitin-60S ribosomal protein L40 / Histone H4 / Histone H2A
Similarity search - Component
Biological speciesChaetomium thermophilum (fungus) / synthetic construct (others) / Xenopus laevis (African clawed frog) / Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.1 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.
History
DepositionJul 24, 2019-
Header (metadata) releaseAug 21, 2019-
Map releaseAug 28, 2019-
UpdateSep 4, 2019-
Current statusSep 4, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6px3
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20517.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 240 pix.
= 249.6 Å
1.04 Å/pix.
x 240 pix.
= 249.6 Å
1.04 Å/pix.
x 240 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.04 Å
Density
Contour LevelBy AUTHOR: 0.01 / Movie #1: 0.01
Minimum - Maximum-0.03748628 - 0.08154655
Average (Standard dev.)0.0010172646 (±0.0035177844)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.041.041.04
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-13-52-30
NX/NY/NZ576659
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0370.0820.001

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Supplemental data

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Sample components

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Entire Set2 bound to ubiquitinated nucleosome

EntireName: Set2 bound to ubiquitinated nucleosome / Number of Components: 12

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Component #1: protein, Set2 bound to ubiquitinated nucleosome

ProteinName: Set2 bound to ubiquitinated nucleosome / Recombinant expression: No
MassTheoretical: 260 kDa

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Component #2: protein, Histone-lysine N-methyltransferase

ProteinName: Histone-lysine N-methyltransferaseHistone methyltransferase
Recombinant expression: No
SourceSpecies: Chaetomium thermophilum (fungus)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, DNA

ProteinName: DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: synthetic construct (others)

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Component #4: protein, Histone H3, Histone H4, Ubiquitin-60S ribosomal protein ...

ProteinName: Histone H3, Histone H4, Ubiquitin-60S ribosomal protein L40,Histone H2A, Histone H2B 1.1
Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, Histone H3

ProteinName: Histone H3 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 15.437144 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, Histone H4

ProteinName: Histone H4 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 11.394426 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: protein, Ubiquitin-60S ribosomal protein L40,Histone H2A

ProteinName: Ubiquitin-60S ribosomal protein L40,Histone H2A / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 24.045436 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #8: protein, Histone H2B 1.1

ProteinName: Histone H2B 1.1 / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 13.655948 kDa
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #9: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (DC)(DT)(DG)(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) ...Sequence:
(DC)(DT)(DG)(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)
MassTheoretical: 45.764141 kDa
SourceSpecies: synthetic construct (others)

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Component #10: nucleic-acid, DNA (145-MER)

nucleic acidName: DNA (145-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence: (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) ...Sequence:
(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)(DC)(DA)(DG)
MassTheoretical: 46.222434 kDa
SourceSpecies: synthetic construct (others)

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Component #11: protein, Histone-lysine N-methyltransferase

ProteinName: Histone-lysine N-methyltransferaseHistone methyltransferase
Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 105.425906 kDa
SourceSpecies: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719) (fungus)
Strain: DSM 1495 / CBS 144.50 / IMI 039719
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #12: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 3 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen State: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen Name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron Source: FIELD EMISSION GUN / Accelerating Voltage: 300 kV / Electron Dose: 75 e/Å2 / Illumination Mode: FLOOD BEAM
LensImaging Mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 BASE (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of Projections: 67000
3D reconstructionResolution: 4.1 Å / Resolution Method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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