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- EMDB-22693: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-22693
TitleNoncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
Map dataInactive conformation Dot1 bound to the H4 unacetylated nucleosome
Sample
  • Complex: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
    • Complex: Histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Histone-lysine N-methyltransferase, H3 lysine-79 specific
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specific
    • Complex: Polyubiquitin-B
      • Protein or peptide: Polyubiquitin-B
    • Complex: DNA (146-MER)
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)
Function / homology
Function and homology information


negative regulation of heterochromatin formation / PKMTs methylate histone lysines / meiotic recombination checkpoint signaling / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / global genome nucleotide-excision repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / recombinational repair ...negative regulation of heterochromatin formation / PKMTs methylate histone lysines / meiotic recombination checkpoint signaling / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / histone H3K79 trimethyltransferase activity / global genome nucleotide-excision repair / postreplication repair / mitotic intra-S DNA damage checkpoint signaling / recombinational repair / subtelomeric heterochromatin formation / mitotic G1 DNA damage checkpoint signaling / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / Downregulation of ERBB4 signaling / p75NTR recruits signalling complexes / APC-Cdc20 mediated degradation of Nek2A / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NF-kB is activated and signals survival / VLDLR internalisation and degradation / Pexophagy / NRIF signals cell death from the nucleus / Regulation of PTEN localization / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / TICAM1, RIP1-mediated IKK complex recruitment / Translesion synthesis by POLK / Downregulation of TGF-beta receptor signaling / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / Translesion synthesis by POLI / Gap-filling DNA repair synthesis and ligation in GG-NER / InlB-mediated entry of Listeria monocytogenes into host cell / Josephin domain DUBs / Regulation of activated PAK-2p34 by proteasome mediated degradation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / IKK complex recruitment mediated by RIP1 / PINK1-PRKN Mediated Mitophagy / DNA damage checkpoint signaling / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / TNFR1-induced NF-kappa-B signaling pathway / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / TCF dependent signaling in response to WNT / Asymmetric localization of PCP proteins / SCF-beta-TrCP mediated degradation of Emi1 / NIK-->noncanonical NF-kB signaling / Ubiquitin-dependent degradation of Cyclin D / Regulation of NF-kappa B signaling / AUF1 (hnRNP D0) binds and destabilizes mRNA / activated TAK1 mediates p38 MAPK activation / TNFR2 non-canonical NF-kB pathway / Negative regulators of DDX58/IFIH1 signaling / NOTCH3 Activation and Transmission of Signal to the Nucleus / Vpu mediated degradation of CD4 / nucleotide-excision repair / Deactivation of the beta-catenin transactivating complex / Assembly of the pre-replicative complex / Regulation of signaling by CBL / Degradation of DVL / Ubiquitin Mediated Degradation of Phosphorylated Cdc25A / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / Dectin-1 mediated noncanonical NF-kB signaling / Fanconi Anemia Pathway / Negative regulation of FGFR3 signaling / Peroxisomal protein import / Hh mutants are degraded by ERAD / Degradation of AXIN / Recognition of DNA damage by PCNA-containing replication complex / Stabilization of p53
Similarity search - Function
Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / Histone H2B signature. / Histone H2B / Histone H2B / Histone H2A conserved site / Histone H2A signature. ...Histone H3-K79 methyltransferase, fungi / Histone-lysine N-methyltransferase DOT1 domain / Histone H3-K79 methyltransferase / Histone methylation protein DOT1 / Histone-lysine N-methyltransferase DOT1 (EC 2.1.1.43) domain profile. / 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 H2A / Histone 2A / Histone H4, conserved site / Histone H4 signature. / TATA box binding protein associated factor / TATA box binding protein associated factor (TAF), histone-like fold domain / Histone H4 / Histone H4 / CENP-T/Histone H4, histone fold / Centromere kinetochore component CENP-T histone fold / Histone H3 signature 1. / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / : / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Ubiquitin domain signature. / Ubiquitin conserved site / Ubiquitin domain / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin domain profile. / Ubiquitin-like domain / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Histone H2B 1.1 / Histone H2A type 1 / Polyubiquitin-C / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast) / Xenopus laevis (African clawed frog) / Homo sap (brewer's yeast) / Synthetic (others) / Xenopus lenduensis (Lendu Plateau clawed frog) / Homo sapiens (human) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 Å
AuthorsValencia-Sanchez MI / De Ioannes PE / Miao W / Truong DM / Lee R / Armache J-P / Boeke JD / Armache K-J
Funding support United States, 2 items
OrganizationGrant numberCountry
David and Lucile Packard Foundation United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)5R01GM115882-03 United States
CitationJournal: Science / Year: 2021
Title: Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.
Authors: Marco Igor Valencia-Sánchez / Pablo De Ioannes / Miao Wang / David M Truong / Rachel Lee / Jean-Paul Armache / Jef D Boeke / Karim-Jean Armache /
Abstract: Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide ...Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.
History
DepositionSep 21, 2020-
Header (metadata) releaseFeb 10, 2021-
Map releaseFeb 10, 2021-
UpdateFeb 10, 2021-
Current statusFeb 10, 2021Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 5
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 5
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_22693.png

Downloads & links

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Map

FileDownload / File: emd_22693.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationInactive conformation Dot1 bound to the H4 unacetylated nucleosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.04 Å/pix.
x 300 pix.
= 310.5 Å		1.04 Å/pix.
x 300 pix.
= 310.5 Å		1.04 Å/pix.
x 300 pix.
= 310.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.035 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.6 / Movie #1: 5
Minimum - Maximum-9.063707 - 28.505844
Average (Standard dev.)0.005038012 (±1.0112352)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 310.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0351.0351.035
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z310.500310.500310.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS300300300
D min/max/mean-9.06428.5060.005

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Supplemental data

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Half map: Half map Inactive conformation Dot1 bound to the...

Fileemd_22693_half_map_1.map
AnnotationHalf map Inactive conformation Dot1 bound to the H4 unacetylated nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map Inactive conformation Dot1 bound to the...

Fileemd_22693_half_map_2.map
AnnotationHalf map Inactive conformation Dot1 bound to the H4 unacetylated nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome

EntireName: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
Components
  • Complex: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
    • Complex: Histones
      • Protein or peptide: Histone H3.2
      • Protein or peptide: Histone H4
      • Protein or peptide: Histone H2A type 1
      • Protein or peptide: Histone H2B 1.1
    • Complex: Histone-lysine N-methyltransferase, H3 lysine-79 specific
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specific
    • Complex: Polyubiquitin-B
      • Protein or peptide: Polyubiquitin-B
    • Complex: DNA (146-MER)
      • DNA: DNA (146-MER)
      • DNA: DNA (146-MER)

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Supramolecule #1: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome

SupramoleculeName: Noncatalytic conformation Dot1 bound to the unacetylated H4 nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: H2BK120 Ubiquitinated H3K79M
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #2: Histones

SupramoleculeName: Histones / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: Histone-lysine N-methyltransferase, H3 lysine-79 specific

SupramoleculeName: Histone-lysine N-methyltransferase, H3 lysine-79 specific
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #5
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: Polyubiquitin-B

SupramoleculeName: Polyubiquitin-B / type: complex / ID: 4 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sap (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #5: DNA (146-MER)

SupramoleculeName: DNA (146-MER) / type: complex / ID: 5 / Parent: 1 / Macromolecule list: #7-#8
Source (natural)Organism: Synthetic (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Histone H3.2

MacromoleculeName: Histone H3.2 / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Xenopus lenduensis (Lendu Plateau clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
KPHRYRPGTV ALRE IRRYQ KSTELLIRKL PFQRLVREIA QDFMTDLRFQ SSAVMALQEA SEAYL VALF EDTNLCAIHA KRVTIMPKDI QLARRIRGER

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Macromolecule #2: Histone H4

MacromoleculeName: Histone H4 / type: protein_or_peptide / ID: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GGAKRHRKVL RDNIQGITKP AIRRLARRGG VKRISGLI Y EETRGVLKVF LENVIRDAVT YTEHAKRKTV TAMDVVYALK RQGRTLYGFG

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKAKTRSSRA GLQFPVGRVH RLLRKGNYAE RVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRND EELNKLLGRV TIAQGGVLP NIQSVLLPK

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Macromolecule #4: Histone H2B 1.1

MacromoleculeName: Histone H2B 1.1 / type: protein_or_peptide / ID: 4 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
TRKESYAIYV YKVLKQVHPD TG ISSKAMS IMNSFVNDVF ERIAGEASRL AHYNKRSTIT SREIQTAVRL LLP GELAKH AVSEGTKAVT KYTSA

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Macromolecule #5: Histone-lysine N-methyltransferase, H3 lysine-79 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-79 specific
type: protein_or_peptide / ID: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: SSTFVDWNGP CLRLQYPLFD IEYLR SHEI YSGTPIQSIS LRTTAKLQSI LFSNYMEEYK VDFKRSTAIY NPMSEI GKL IEYSCLVFLP SPYAEQLKET ILPDLNASFD NSDTKGFVNA INLYNKM IR EIPRQRIIDH LETIDKIPRS FIHDFLHIVY TRSIHPQANK ...String:
SSTFVDWNGP CLRLQYPLFD IEYLR SHEI YSGTPIQSIS LRTTAKLQSI LFSNYMEEYK VDFKRSTAIY NPMSEI GKL IEYSCLVFLP SPYAEQLKET ILPDLNASFD NSDTKGFVNA INLYNKM IR EIPRQRIIDH LETIDKIPRS FIHDFLHIVY TRSIHPQANK LKHYKAFS N YVYGELLPNF LSDVYQQCQL KKGDTFMDLG SGVGNCVVQA ALECGCALS FGCEIMDDAS DLTILQYEEL KKRCKLYGMR LNNVEFSLKK SFVDNNRVAE LIPQCDVIL VNNFLFDEDL NKKVEKILQT AKVGCKIISL KSLRSLTYQI N FYNVENIF NRLKVQRYDL KEDSVSWTHS GGEYYISTVM EDVDESLFSP AA RGRRPVK YM

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Macromolecule #6: Polyubiquitin-B

MacromoleculeName: Polyubiquitin-B / type: protein_or_peptide / ID: 6 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MQIFVKTLTG KTITLEVEPS DTIENVKAKI QDKEGIPPDQ QRLIFAGKQL EDGRTLSDYN IQKESTLHLV LRLRGC

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Macromolecule #7: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 7 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
TCGAGAATCC CGGTGCCGAG GCCGCTCAAT TGGTCGTAGA CAGCTCTAG CACCGCTTAA ACGCACGTAC GGATTCTCCC CCGCGTTTTA ACCGCCAAGG GGATTACTC CCTAGTCTCC AGGCACGTGT CAGATATATA CATCCGAT

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Macromolecule #8: DNA (146-MER)

MacromoleculeName: DNA (146-MER) / type: dna / ID: 8 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
SequenceString:
ATCGGATGTA TATATCTGAC ACGTGCCTGG AGACTAGGGA GTAATCCCCT TGGCGGTTA AAACGCGGGG GAGAATCCGT ACGTGCGTTT AAGCGGTGCT A GAGCTGTC TACGACCAAT TGAGCGGCCT CGGCACCGGG ATTCTCGA

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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

Concentration0.45 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMTrisTris
50.0 mMKClKCl
1.0 mMMgCl2MgCl2
1.0 mMDTTDTT
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 297 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Sampling interval: 5.0 µm / Number grids imaged: 1 / Number real images: 4031 / Average exposure time: 8.0 sec. / Average electron dose: 52.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1673215
CTF correctionSoftware - Name: Gctf (ver. 1.18)
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

1u2z


Details: 1U2Z 3TU4 1UBQ
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 2.15) / Number images used: 119673
Initial angle assignmentType: OTHER / Software - Name: cryoSPARC (ver. 2.15) / Details: Ab initio in CryoSparc
Final angle assignmentType: PROJECTION MATCHING / Software - Name: cisTEM (ver. 1.0)
Final 3D classificationNumber classes: 3 / Software - Name: cryoSPARC (ver. 2.15)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1u2z

chain_id: A

3tu4


1ubq

chain_id: A
RefinementSpace: REAL / Protocol: RIGID BODY FIT

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