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- EMDB-41111: Catalytic and non-catalytic mechanisms of histone H4 lysine 20 me... -

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Entry
Database: EMDB / ID: EMD-41111
TitleCatalytic and non-catalytic mechanisms of histone H4 lysine 20 methyltransferase SUV420H1
Map data
Sample
  • Complex: SUV420H1-H2A.Z nucleosome complex
    • Protein or peptide: Histone-lysine N-methyltransferase KMT5B
    • DNA: DNA (146-MER)
    • DNA: DNA (146-MER)
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H3.2
  • Protein or peptide: Histone H2A
  • Protein or peptide: Histone H2B 1.1
KeywordsChromatin / Histone H4 modification / Methyltransferase / GENE REGULATION
Function / homology
Function and homology information


[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development ...[histone H4]-N-methyl-L-lysine20 N-methyltransferase / histone H4K20me methyltransferase activity / [histone H4]-lysine20 N-methyltransferase / histone H4K20 monomethyltransferase activity / histone H4K20 methyltransferase activity / histone H4 methyltransferase activity / positive regulation of isotype switching / condensed chromosome, centromeric region / S-adenosyl-L-methionine binding / muscle organ development / positive regulation of double-strand break repair via nonhomologous end joining / histone methyltransferase activity / PKMTs methylate histone lysines / structural constituent of chromatin / nucleosome / nucleosome assembly / methylation / protein heterodimerization activity / DNA repair / chromatin binding / DNA binding / nucleoplasm / nucleus / metal ion binding
Similarity search - Function
KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain ...KMT5B , SET domain / Suv4-20 family, animal / Histone-lysine N-methyltransferase Suv4-20/Set9 / Histone-lysine N-methyltransferase, N-terminal domain / Histone-lysine N-methyltransferase (EC 2.1.1.43) family profile. / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain / SET domain superfamily / SET domain profile. / SET domain / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. / Histone H2A, C-terminal domain / C-terminus of histone H2A / Histone H4, conserved site / Histone H4 signature. / Histone H4 / Histone H4 / Histone H2A / Histone 2A / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold
Similarity search - Domain/homology
Histone H4 / Histone H2B 1.1 / Histone H3.2 / Histone-lysine N-methyltransferase KMT5B / Histone H2A
Similarity search - Component
Biological speciesXenopus laevis (African clawed frog) / Homo sapiens (human) / Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.37 Å
AuthorsAbini-Agbomson S / Armache K-J
Funding support United States, 4 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM115882 United States
The Mark Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5T32GM088118 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01CA266978 United States
CitationJournal: bioRxiv / Year: 2023
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 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 Simon / Jean-Paul Armache / Evgeny Nudler / Geeta Narlikar / Shixin Liu / Chao Lu / Karim-Jean Armache /
Abstract: The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of ...The intricate regulation of chromatin plays a key role in controlling genome architecture and accessibility. Histone lysine methyltransferases regulate chromatin by catalyzing the methylation of specific histone residues but are also hypothesized to have equally important non-catalytic roles. SUV420H1 di- and tri-methylates histone H4 lysine 20 (H4K20me2/me3) and plays crucial roles in DNA replication, repair, and heterochromatin formation, and 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 the enzyme likely has uncharacterized non-catalytic activities. To characterize the catalytic and non-catalytic mechanisms SUV420H1 uses to modify chromatin, we determined cryo- EM structures of SUV420H1 complexes with nucleosomes containing histone H2A or its variant H2A.Z. Our structural, biochemical, biophysical, and cellular analyses reveal how both SUV420H1 recognizes its substrate and H2A.Z stimulates its activity, and show that SUV420H1 binding to nucleosomes causes a dramatic detachment of nucleosomal DNA from histone octamer. We hypothesize that this detachment increases DNA accessibility to large macromolecular complexes, a prerequisite for DNA replication and repair. We also show that SUV420H1 can promote chromatin condensates, another non-catalytic role 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
DepositionJun 24, 2023-
Header (metadata) releaseSep 13, 2023-
Map releaseSep 13, 2023-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_41111.png

Downloads & links

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Map

FileDownload / File: emd_41111.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å		1.1 Å/pix.
x 320 pix.
= 350.72 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.096 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.22
Minimum - Maximum-0.41419527 - 1.2945656
Average (Standard dev.)-0.0006690846 (±0.031569853)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 350.71997 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_41111_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_41111_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : SUV420H1-H2A.Z nucleosome complex

EntireName: SUV420H1-H2A.Z nucleosome complex
Components
  • Complex: SUV420H1-H2A.Z nucleosome complex
    • Protein or peptide: Histone-lysine N-methyltransferase KMT5B
    • DNA: DNA (146-MER)
    • DNA: DNA (146-MER)
    • Protein or peptide: Histone H4
    • Protein or peptide: Histone H3.2
  • Protein or peptide: Histone H2A
  • Protein or peptide: Histone H2B 1.1

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Supramolecule #1: SUV420H1-H2A.Z nucleosome complex

SupramoleculeName: SUV420H1-H2A.Z nucleosome complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #7, #5-#6, #2, #1
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 15.30393 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
ARTKQTARKS TGGKAPRKQL ATKAARKSAP ATGGVKKPHR YRPGTVALRE IRRYQKSTEL LIRKLPFQRL VREIAQDFKT DLRFQSSAV MALQEASEAY LVALFEDTNL CAIHAKRVTI MPKDIQLARR IRGERA

UniProtKB: Histone H3.2

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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: 11.396442 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKGGKG LGKGGAKRHR MVLRDNIQGI TKPAIRRLAR RGGVKRISGL IYEETRGVLK VFLENVIRDA VTYTEHAKRK TVTAMDVVY ALKRQGRTLY GFGG

UniProtKB: Histone H4

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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: 14.109436 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MSGRGKQGGK TRAKAKTRSS RAGLQFPVGR VHRLLRKGNY AERVGAGAPV YLAAVLEYLT AEILELAGNA ARDNKKTRII PRHLQLAVR NDEELNKLLG RVTIAQGGVL PNIQSVLLPK KTESSKSAKS K

UniProtKB: Histone H2A

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.655948 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString:
MAKSAPAPKK GSKKAVTKTQ KKDGKKRRKT RKESYAIYVY KVLKQVHPDT GISSKAMSIM NSFVNDVFER IAGEASRLAH YNKRSTITS REIQTAVRLL LPGELAKHAV SEGTKAVTKY TSAK

UniProtKB: Histone H2B 1.1

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Macromolecule #7: Histone-lysine N-methyltransferase KMT5B

MacromoleculeName: Histone-lysine N-methyltransferase KMT5B / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 44.703094 KDa
Recombinant expressionOrganism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
SequenceString: GSKWLGESKN MVVNGRRNGG KLSNDHQQNQ SKLQHTGKDT LKAGKNAVER RSNRCNGNSG FEGQSRYVPS SGMSAKELCE NDDLATSLV LDPYLGFQTH KMNTSAFPSR SSRHFSKSDS FSHNNPVRFR PIKGRQEELK EVIERFKKDE HLEKAFKCLT S GEWARHYF ...String:
GSKWLGESKN MVVNGRRNGG KLSNDHQQNQ SKLQHTGKDT LKAGKNAVER RSNRCNGNSG FEGQSRYVPS SGMSAKELCE NDDLATSLV LDPYLGFQTH KMNTSAFPSR SSRHFSKSDS FSHNNPVRFR PIKGRQEELK EVIERFKKDE HLEKAFKCLT S GEWARHYF LNKNKMQEKL FKEHVFIYLR MFATDSGFEI LPCNRYSSEQ NGAKIVATKE WKRNDKIELL VGCIAELSEI EE NMLLRHG ENDFSVMYST RKNCAQLWLG PAAFINHDCR PNCKFVSTGR DTACVKALRD IEPGEEISCY YGDGFFGENN EFC ECYTCE RRGTGAFKSR VGLPAPAPVI NSKYGLRETD KRLNRLKKLG DSSKNSDSQS VSSNTDADTT QEKNNASK

UniProtKB: Histone-lysine N-methyltransferase KMT5B

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Macromolecule #5: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 5 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 44.82457 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)(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)

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Macromolecule #6: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 6 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Molecular weightTheoretical: 45.304863 KDa
SequenceString: (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)

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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: 7.9
Component:
ConcentrationFormulaName
100.0 mMNaClSodium chloride
50.0 mMC8H18N2O4SHEPES
2.0 mMC4H10O2S2DTT

Details: 50 mM HEPES pH 7.9, 100 mM NaCl, 2 mM DTT
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.37 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 366390
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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