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- EMDB-31039: Yeast Set2 bound to a nucleosome containing oncohistone mutations -

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Basic information

Entry
Database: EMDB / ID: EMD-31039
TitleYeast Set2 bound to a nucleosome containing oncohistone mutations
Map data
Sample
  • Complex: The Set2-nucleosome(H3K36M)complex structure
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 601-DNA
    • DNA: 601-DNA
    • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-36 specific
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINE
Keywordsmethyltransferase / Set2 / nucleosome / H3K36M mutation / GENE REGULATION
Function / homology
Function and homology information


[histone H3]-lysine36 N-trimethyltransferase / histone H3K36 methyltransferase activity / structural constituent of chromatin / nucleosome / heterochromatin formation / chromosome / protein heterodimerization activity / regulation of DNA-templated transcription / DNA binding / nucleus
Similarity search - Function
WW domain / Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. ...WW domain / Histone-lysine N-methyltransferase, Set2, fungi / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / Set2 Rpb1 interacting domain superfamily / SETD2/Set2, SET domain / Set2 Rpb1 interacting domain / SRI (Set2 Rpb1 interacting) domain / AWS domain / AWS domain / AWS domain profile. / associated with SET domains / Cysteine-rich motif following a subset of SET domains / Post-SET domain / Post-SET domain profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / WW domain superfamily / SET domain / Domain with 2 conserved Trp (W) residues / SET domain profile. / SET domain / WW domain / : / Histone H2B signature. / Histone H2A conserved site / Histone H2A signature. / Histone H2B / Histone H2B / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone 2A / Histone H2A / 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
Histone H2B / Histone H3 / Histone-lysine N-methyltransferase, H3 lysine-36 specific / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Saccharomyces cerevisiae (brewer's yeast) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsJing H / Liu Y
Funding support China, 3 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32022036 China
National Natural Science Foundation of China (NSFC)31570766 China
National Natural Science Foundation of China (NSFC)U1632130 China
CitationJournal: Cell Discov / Year: 2021
Title: Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations.
Authors: Yingying Liu / Yanjun Zhang / Han Xue / Mi Cao / Guohui Bai / Zongkai Mu / Yanli Yao / Shuyang Sun / Dong Fang / Jing Huang /
Abstract: Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone ...Substitution of lysine 36 with methionine in histone H3.3 (H3.3K36M) is an oncogenic mutation that inhibits SETD2-mediated histone H3K36 tri-methylation in tumors. To investigate how the oncohistone mutation affects the function of SETD2 at the nucleosome level, we determined the cryo-EM structure of human SETD2 associated with an H3.3K36M nucleosome and cofactor S-adenosylmethionine (SAM), and revealed that SETD2 is attached to the N-terminal region of histone H3 and the nucleosome DNA at superhelix location 1, accompanied with the partial unwrapping of nucleosome DNA to expose the SETD2-binding site. These structural features were also observed in the previous cryo-EM structure of the fungal Set2-nucleosome complex. By contrast with the stable association of SETD2 with the H3.3K36M nucleosome, the EM densities of SETD2 could not be observed on the wild-type nucleosome surface, suggesting that the association of SETD2 with wild-type nucleosome might be transient. The linker histone H1, which stabilizes the wrapping of nucleosome DNA at the entry/exit sites, exhibits an inhibitory effect on the activities of SETD2 and displays inversely correlated genome distributions with that of the H3K36me3 marks. Cryo-EM analysis of yeast H3K36 methyltransferase Set2 complexed with nucleosomes further revealed evolutionarily conserved structural features for nucleosome recognition in eukaryotes, and provides insights into the mechanism of activity regulation. These findings have advanced our understanding of the structural basis for the tumorigenesis mechanism of the H3.3K36M mutation and highlight the effect of nucleosome conformation on the regulation of histone modification.
History
DepositionMar 6, 2021-
Header (metadata) releaseJul 14, 2021-
Map releaseJul 14, 2021-
UpdateSep 17, 2025-
Current statusSep 17, 2025Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-7ea5
  • Surface level: 0.0165
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_31039.png

Downloads & links

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Map

FileDownload / File: emd_31039.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.)
1.09 Å/pix.
x 240 pix.
= 261.6 Å		1.09 Å/pix.
x 240 pix.
= 261.6 Å		1.09 Å/pix.
x 240 pix.
= 261.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.09 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0165 / Movie #1: 0.0165
Minimum - Maximum-0.09487605 - 0.16799808
Average (Standard dev.)-0.000027337112 (±0.0048009627)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 261.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.091.091.09
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z261.600261.600261.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ256256256
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0950.168-0.000

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Supplemental data

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Sample components

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Entire : The Set2-nucleosome(H3K36M)complex structure

EntireName: The Set2-nucleosome(H3K36M)complex structure
Components
  • Complex: The Set2-nucleosome(H3K36M)complex structure
    • Protein or peptide: Histone H3
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H2A
    • Protein or peptide: Histone H2B
    • DNA: 601-DNA
    • DNA: 601-DNA
    • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-36 specific
  • Ligand: ZINC ION
  • Ligand: S-ADENOSYLMETHIONINE

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Supramolecule #1: The Set2-nucleosome(H3K36M)complex structure

SupramoleculeName: The Set2-nucleosome(H3K36M)complex structure / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3

MacromoleculeName: Histone H3 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.847916 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString:
GVMKPHRYRP GTVALREIRR YQKSTELLIR KLPFQRLVRE IAQDFKTDLR FQSSAVMALQ EASEAYLVAL FEDTNLCAIH AKRVTIMPK DIQLARRIRG ER

UniProtKB: Histone H3

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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: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 8.853342 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
DNIQGITKPA IRRLARRGGV KRISGLIYEE TRGVLKVFLE NVIRDAVTYT EHAKRKTVTA MDVVYALKRQ GRTLYGFG

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Macromolecule #3: Histone H2A

MacromoleculeName: Histone H2A / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 11.494393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KAKTRSSRAG LQFPVGRVHR LLRKGNYAER VGAGAPVYLA AVLEYLTAEI LELAGNAARD NKKTRIIPRH LQLAVRNDEE LNKLLGRVT IAQGGVLPNI QSVLLP

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B

MacromoleculeName: Histone H2B / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 10.406954 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString:
KTRKESYAIY VYKVLKQVHP DTGISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLPGELAKHA VSEGTKAVT KYTS

UniProtKB: Histone H2B

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Macromolecule #7: Histone-lysine N-methyltransferase, H3 lysine-36 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-36 specific
type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO / EC number: [histone H3]-lysine36 N-trimethyltransferase
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Molecular weightTheoretical: 26.699021 KDa
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: EPDLTEEALT KFENLDDCIY ANKRIGTFKN NDFMECDCYE EFSDGVNHAC DEDSDCINRL TLIECVNDLC SSCGNDCQNQ RFQKKQYAP IAIFKTKHKG YGVRAEQDIE ANQFIYEYKG EVIEEMEFRD RLIDYDQRHF KHFYFMMLQN GEFIDATIKG S LARFCNHS ...String:
EPDLTEEALT KFENLDDCIY ANKRIGTFKN NDFMECDCYE EFSDGVNHAC DEDSDCINRL TLIECVNDLC SSCGNDCQNQ RFQKKQYAP IAIFKTKHKG YGVRAEQDIE ANQFIYEYKG EVIEEMEFRD RLIDYDQRHF KHFYFMMLQN GEFIDATIKG S LARFCNHS CSPNAYVNKW VVKDKLRMGI FAQRKILKGE EITFDYNVDR YGAQAQKCYC EEPNCIGFLG

UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-36 specific

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Macromolecule #5: 601-DNA

MacromoleculeName: 601-DNA / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.521367 KDa
SequenceString: (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) ...String:
(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) (DG)(DA)

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Macromolecule #6: 601-DNA

MacromoleculeName: 601-DNA / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.992648 KDa
SequenceString: (DT)(DC)(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) ...String:
(DT)(DC)(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)

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 3 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #9: S-ADENOSYLMETHIONINE

MacromoleculeName: S-ADENOSYLMETHIONINE / type: ligand / ID: 9 / Number of copies: 1 / Formula: SAM
Molecular weightTheoretical: 398.437 Da
Chemical component information

ChemComp-SAM:
S-ADENOSYLMETHIONINE

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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

Concentration0.3 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: EMDB MAP
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 225474
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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