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- EMDB-0468: Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome -

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Basic information

Entry
Database: EMDB / ID: EMD-0468
TitlePoised-state Dot1L bound to the H2B-Ubiquitinated nucleosome
Map dataSharpened map of poised state dot1L bound to the H2B-Ub nucleosome
Sample
  • Complex: Poised state Dot1L in complex with the H2B-Ub nucleosome
    • Complex: Dot1L
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
    • Complex: H2B-Ub nucleosome
      • Complex: histone core
        • 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: ubiquitin
        • Protein or peptide: Ubiquitin
      • Complex: DNA
        • DNA: 601 DNA Strand 1
        • DNA: 601 DNA Strand 2
KeywordsUbiquitin / Nucleosome / Methyltransferase / STRUCTURAL PROTEIN-TRANSFERASE-DNA complex
Function / homology
Function and homology information


: / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization ...: / histone H3K79 trimethyltransferase activity / [histone H3]-lysine79 N-trimethyltransferase / histone H3K79 methyltransferase activity / regulation of transcription regulatory region DNA binding / histone H3 methyltransferase activity / regulation of receptor signaling pathway via JAK-STAT / histone methyltransferase activity / heterochromatin formation / telomere organization / DNA damage checkpoint signaling / PKMTs methylate histone lysines / structural constituent of chromatin / nucleosome / gene expression / RNA polymerase II-specific DNA-binding transcription factor binding / nucleic acid binding / transcription coactivator activity / protein heterodimerization activity / DNA repair / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
Histone H3-K79 methyltransferase, metazoa / 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, metazoa / 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. / Histone H4 / Histone H4 / 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. / Ubiquitin conserved site / Ubiquitin domain / Histone H3 signature 2. / Histone H3 / Histone H3/CENP-A / Ubiquitin domain signature. / Histone H2A/H2B/H3 / Core histone H2A/H2B/H3/H4 / Histone-fold / Ubiquitin family / Ubiquitin homologues / Ubiquitin-like domain / Ubiquitin domain profile. / Ubiquitin-like domain superfamily / S-adenosyl-L-methionine-dependent methyltransferase superfamily
Similarity search - Domain/homology
Ubiquitin B / Histone H2B 1.1 / Histone H2A type 1 / Histone H4 / Histone H3.2 / Histone-lysine N-methyltransferase, H3 lysine-79 specific
Similarity search - Component
Biological speciesHomo sapiens (human) / Xenopus laevis (African clawed frog) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsWorden EJ / Hoffmann NA
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM095822 United States
CitationJournal: Cell / Year: 2019
Title: Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L.
Authors: Evan J Worden / Niklas A Hoffmann / Chad W Hicks / Cynthia Wolberger /
Abstract: Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is ...Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
History
DepositionJan 16, 2019-
Header (metadata) releaseFeb 6, 2019-
Map releaseFeb 20, 2019-
UpdateMar 20, 2024-
Current statusMar 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6nog
  • Surface level: 0.0184
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0468.png

Downloads & links

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Map

FileDownload / File: emd_0468.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened map of poised state dot1L bound to the H2B-Ub nucleosome
Voxel sizeX=Y=Z: 1.064 Å
Density
Contour LevelBy AUTHOR: 0.0184 / Movie #1: 0.0184
Minimum - Maximum-0.052451484 - 0.09601253
Average (Standard dev.)0.00033886472 (±0.0028687266)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 272.384 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0641.0641.064
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z272.384272.384272.384
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0520.0960.000

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Supplemental data

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Mask #1

Fileemd_0468_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unsharpened map of poised state dot1L bound to the H2B-Ub nucleosome

Fileemd_0468_additional.map
AnnotationUnsharpened map of poised state dot1L bound to the H2B-Ub nucleosome
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Sharpened half map used for structure refinement

Fileemd_0468_half_map_1.map
AnnotationSharpened half map used for structure refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Sharpened half map used for structure validation

Fileemd_0468_half_map_2.map
AnnotationSharpened half map used for structure validation
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Poised state Dot1L in complex with the H2B-Ub nucleosome

EntireName: Poised state Dot1L in complex with the H2B-Ub nucleosome
Components
  • Complex: Poised state Dot1L in complex with the H2B-Ub nucleosome
    • Complex: Dot1L
      • Protein or peptide: Histone-lysine N-methyltransferase, H3 lysine-79 specificHistone methyltransferase
    • Complex: H2B-Ub nucleosome
      • Complex: histone core
        • 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: ubiquitin
        • Protein or peptide: Ubiquitin
      • Complex: DNA
        • DNA: 601 DNA Strand 1
        • DNA: 601 DNA Strand 2

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Supramolecule #1: Poised state Dot1L in complex with the H2B-Ub nucleosome

SupramoleculeName: Poised state Dot1L in complex with the H2B-Ub nucleosome
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all / Details: 1:1 complex of Dot1L bound to the nucleosome

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Supramolecule #2: Dot1L

SupramoleculeName: Dot1L / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #6
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: H2B-Ub nucleosome

SupramoleculeName: H2B-Ub nucleosome / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #1-#5, #7-#8

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Supramolecule #4: histone core

SupramoleculeName: histone core / type: complex / ID: 4 / Parent: 3 / Macromolecule list: #1-#4
Source (natural)Organism: Xenopus laevis (African clawed frog)

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Supramolecule #5: ubiquitin

SupramoleculeName: ubiquitin / type: complex / ID: 5 / Parent: 3 / Macromolecule list: #5
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #6: DNA

SupramoleculeName: DNA / type: complex / ID: 6 / Parent: 3 / Macromolecule list: #7-#8
Source (natural)Organism: synthetic construct (others)

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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 (E. coli)
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: 11.263231 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKGGKGL GKGGAKRHRK VLRDNIQGIT KPAIRRLARR GGVKRISGLI YEETRGVLKV FLENVIRDAV TYTEHAKRKT VTAMDVVYA LKRQGRTLYG FGG

UniProtKB: Histone H4

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Macromolecule #3: Histone H2A type 1

MacromoleculeName: Histone H2A type 1 / type: protein_or_peptide / ID: 3 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Xenopus laevis (African clawed frog)
Molecular weightTheoretical: 13.978241 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
SGRGKQGGKT RAKAKTRSSR AGLQFPVGRV HRLLRKGNYA ERVGAGAPVY LAAVLEYLTA EILELAGNAA RDNKKTRIIP RHLQLAVRN DEELNKLLGR VTIAQGGVLP NIQSVLLPKK TESSKSAKSK

UniProtKB: Histone H2A type 1

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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: 13.498715 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
AKSAPAPKKG SKKAVTKTQK KDGKKRRKTR KESYAIYVYK VLKQVHPDTG ISSKAMSIMN SFVNDVFERI AGEASRLAHY NKRSTITSR EIQTAVRLLL PGELAKHAVS EGTKAVTCYT SAK

UniProtKB: Histone H2B 1.1

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Macromolecule #5: Ubiquitin

MacromoleculeName: Ubiquitin / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 9.036393 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
GSHMMQIFVK TLTGKTITLE VEPSDTIENV KAKIQDKEGI PPDQQRLIFA GKQLEDGRTL SDYNIQKEST LHLVLRLRGC

UniProtKB: Ubiquitin B

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Macromolecule #6: Histone-lysine N-methyltransferase, H3 lysine-79 specific

MacromoleculeName: Histone-lysine N-methyltransferase, H3 lysine-79 specific
type: protein_or_peptide / ID: 6 / Number of copies: 1 / Enantiomer: LEVO / EC number: histone-lysine N-methyltransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 47.432012 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: GGEKLELRLK SPVGAEPAVY PWPLPVYDKH HDAAHEIIET IRWVCEEIPD LKLAMENYVL IDYDTKSFES MQRLCDKYNR AIDSIHQLW KGTTQPMKLN TRPSTGLLRH ILQQVYNHSV TDPEKLNNYE PFSPEVYGET SFDLVAQMID EIKMTDDDLF V DLGSGVGQ ...String:
GGEKLELRLK SPVGAEPAVY PWPLPVYDKH HDAAHEIIET IRWVCEEIPD LKLAMENYVL IDYDTKSFES MQRLCDKYNR AIDSIHQLW KGTTQPMKLN TRPSTGLLRH ILQQVYNHSV TDPEKLNNYE PFSPEVYGET SFDLVAQMID EIKMTDDDLF V DLGSGVGQ VVLQVAAATN CKHHYGVEKA DIPAKYAETM DREFRKWMKW YGKKHAEYTL ERGDFLSEEW RERIANTSVI FV NNFAFGP EVDHQLKERF ANMKEGGRIV SSKPFAPLNF RINSRNLSDI GTIMRVVELS PLKGSVSWTG KPVSYYLHTI DRT ILENYF SSLKNPKLRE EQEAARRRQQ RESKSNAATP TKGPEGKVAG PADAPMDSGA EEEKAGAATV KKPSPSKARK KKLN KKGRK MAGRKRGRPK K

UniProtKB: Histone-lysine N-methyltransferase, H3 lysine-79 specific

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Macromolecule #7: 601 DNA Strand 1

MacromoleculeName: 601 DNA Strand 1 / type: dna / ID: 7 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 44.825559 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)(DT)

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Macromolecule #8: 601 DNA Strand 2

MacromoleculeName: 601 DNA Strand 2 / type: dna / ID: 8 / Number of copies: 1 / Classification: DNA
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 45.305852 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)(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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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.75 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
50.0 mMNaClSodium chloridesodium chloride
2.0 mMC4H10O2S2dithiothreitol
20.0 mMC8H18N2O4SHEPES

Details: Solutions were prepared on the day of freezing and filtered though a 0.2 um filter prior to use.
GridModel: C-flat-2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV / Details: Blot once for 3.5 seconds before freezing.
DetailsCrosslinked with glutaraldehyde

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 130000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 1-40 / Number grids imaged: 1 / Number real images: 2267 / Average exposure time: 9.0 sec. / Average electron dose: 50.0 e/Å2 / Details: 3 exposures per hole
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 578660
Startup modelType of model: INSILICO MODEL
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: RELION (ver. 2.0)
Final 3D classificationNumber classes: 5 / Software - Name: RELION (ver. 3.0)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0)
Final reconstructionNumber classes used: 2 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2.0) / Number images used: 108658
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model
PDB IDChain

1kx3

chain_id: A, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: B, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: C, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: D, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: E, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: F, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: G, source_name: PDB, initial_model_type: experimental model

1kx3

chain_id: H, source_name: PDB, initial_model_type: experimental model

3qow

chain_id: K, source_name: PDB, initial_model_type: experimental model

1ubq

chain_id: L, source_name: PDB, initial_model_type: experimental model

3mvd

chain_id: I, source_name: PDB, initial_model_type: experimental model

3mvd

chain_id: J, source_name: PDB, initial_model_type: experimental model
RefinementSpace: REAL / Protocol: OTHER
Output model

PDB-6nog:
Poised-state Dot1L bound to the H2B-Ubiquitinated nucleosome

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