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- EMDB-41272: Catalytic and non-catalytic mechanisms of histone H4 lysine 20 me... -
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Open data
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Basic information
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Title | Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1 | |||||||||||||||
![]() | Cryo-EM map of H2A.Z nucleosome | |||||||||||||||
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![]() | Chromatin / Histone H4 modification / Methyltransferase / GENE REGULATION / GENE REGULATION-DNA complex | |||||||||||||||
Function / homology | ![]() RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / nucleosomal DNA binding / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly ...RNA polymerase II core promoter sequence-specific DNA binding / heterochromatin / nucleosomal DNA binding / cellular response to estradiol stimulus / euchromatin / heterochromatin formation / chromatin DNA binding / structural constituent of chromatin / nucleosome / nucleosome assembly / chromatin organization / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein heterodimerization activity / Amyloid fiber formation / positive regulation of transcription by RNA polymerase II / DNA binding / extracellular exosome / nucleoplasm / nucleus Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Abini-Agbomson S / Armache K-J | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Catalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1. Authors: Stephen Abini-Agbomson / Kristjan Gretarsson / Rochelle M Shih / Laura Hsieh / Tracy Lou / Pablo De Ioannes / Nikita Vasilyev / Rachel Lee / Miao Wang / Matthew D Simon / Jean-Paul Armache / ...Authors: Stephen Abini-Agbomson / Kristjan Gretarsson / Rochelle M Shih / Laura Hsieh / Tracy Lou / Pablo De Ioannes / Nikita Vasilyev / Rachel Lee / Miao Wang / Matthew D Simon / Jean-Paul Armache / Evgeny Nudler / Geeta Narlikar / Shixin Liu / Chao Lu / Karim-Jean Armache / ![]() Abstract: SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many ...SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/H4K20me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation. It is dysregulated in several cancers. Many of these processes were linked to its catalytic activity. However, deletion and inhibition of SUV420H1 have shown distinct phenotypes, suggesting that the enzyme likely has uncharacterized non-catalytic activities. Our cryoelectron microscopy (cryo-EM), biochemical, biophysical, and cellular analyses reveal how SUV420H1 recognizes its nucleosome substrates, and how histone variant H2A.Z stimulates its catalytic activity. SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from the histone octamer, which is a non-catalytic activity. We hypothesize that this regulates the accessibility of large macromolecular complexes to chromatin. We show that SUV420H1 can promote chromatin condensation, another non-catalytic activity that we speculate is needed for its heterochromatin functions. Together, our studies uncover and characterize the catalytic and non-catalytic mechanisms of SUV420H1, a key histone methyltransferase that plays an essential role in genomic stability. | |||||||||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 19.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 21.8 KB 21.8 KB | Display Display | ![]() |
Images | ![]() | 48.9 KB | ||
Others | ![]() ![]() | 116.1 MB 116.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8thuMC ![]() 8t9fC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM map of H2A.Z nucleosome | ||||||||||||||||||||
Voxel size | X=Y=Z: 0.852 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: Cryo-EM half map of H2A.Z nucleosome
File | emd_41272_half_map_1.map | ||||||||||||
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Annotation | Cryo-EM half map of H2A.Z nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Cryo-EM half map of H2A.Z nucleosome
File | emd_41272_half_map_2.map | ||||||||||||
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Annotation | Cryo-EM half map of H2A.Z nucleosome | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : SUV420H1-H2A.Z nucleosome complex
Entire | Name: SUV420H1-H2A.Z nucleosome complex |
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Components |
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-Supramolecule #1: SUV420H1-H2A.Z nucleosome complex
Supramolecule | Name: SUV420H1-H2A.Z nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#4, #6, #5 |
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Source (natural) | Organism: ![]() |
-Macromolecule #1: Histone H2A.Z
Macromolecule | Name: Histone H2A.Z / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.581796 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAGGKAGKDS GKAKTKAVSR SQRAGLQFPV GRIHRHLKSR TTSHGRVGAT AAVYSAAILE YLTAEVLELA GNASKDLKVK RITPRHLQL AIRGDEELDS LIKATIAGGG VIPHIHKSLI GKKGQQKTV UniProtKB: Histone H2A.Z |
-Macromolecule #2: Histone H3.2
Macromolecule | Name: Histone H3.2 / type: protein_or_peptide / ID: 2 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 15.30393 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA UniProtKB: Histone H3.2 |
-Macromolecule #3: Histone H4
Macromolecule | Name: Histone H4 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 11.394426 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MSGRGKGGKG LGKGGAKRHR KVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG UniProtKB: Histone H4 |
-Macromolecule #4: Histone H2B 1.1
Macromolecule | Name: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 13.655948 KDa |
Recombinant expression | Organism: ![]() ![]() |
Sequence | String: MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK UniProtKB: Histone H2B 1.1 |
-Macromolecule #5: DNA (145-MER)
Macromolecule | Name: DNA (145-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 44.82457 KDa |
Sequence | 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) ...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)(DG)(DA)(DT)(DT)(DC)(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)(DT) |
-Macromolecule #6: DNA (146-MER)
Macromolecule | Name: DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA |
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Source (natural) | Organism: synthetic construct (others) |
Molecular weight | Theoretical: 45.304863 KDa |
Sequence | String: (DA)(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) ...String: (DA)(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)(DG)(DA)(DA)(DT)(DC)(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) |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 0.3 mg/mL | ||||||||||||
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Buffer | pH: 7.9 Component:
Details: 50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT | ||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 206872 |
Initial angle assignment | Type: OTHER |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |