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- EMDB-9127: A nucleosome bridging mechanism for activation of a maintenance D... -

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Basic information

Entry
Database: EMDB / ID: EMD-9127
TitleA nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase
Map dataNegative stain map of ZMET2 in complex with H3Kc9me3 dinucleosome with 20 pase pairs of linker DNA.
Sample
  • Complex: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.
    • Complex: Xenopus histones
    • Complex: ZMET2
    • Complex: 601 dinucleosomal DNA
Biological speciesXenopus laevis (African clawed frog) / Zea mays (maize) / synthetic construct (others)
Methodsingle particle reconstruction / negative staining / Resolution: 28.0 Å
AuthorsStoddard CI / Feng S / Campbell MG / Liu W / Wang H / Zhong X / Bernatavichute Y / Cheng Y / Jacobsen SE / Narlikar GJ
CitationJournal: Mol Cell / Year: 2019
Title: A Nucleosome Bridging Mechanism for Activation of a Maintenance DNA Methyltransferase.
Authors: Caitlin I Stoddard / Suhua Feng / Melody G Campbell / Wanlu Liu / Haifeng Wang / Xuehua Zhong / Yana Bernatavichute / Yifan Cheng / Steven E Jacobsen / Geeta J Narlikar /
Abstract: DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is ...DNA methylation and H3K9me are hallmarks of heterochromatin in plants and mammals, and are successfully maintained across generations. The biochemical and structural basis for this maintenance is poorly understood. The maintenance DNA methyltransferase from Zea mays, ZMET2, recognizes dimethylation of H3K9 via a chromodomain (CD) and a bromo adjacent homology (BAH) domain, which flank the catalytic domain. Here, we show that dinucleosomes are the preferred ZMET2 substrate, with DNA methylation preferentially targeted to linker DNA. Electron microscopy shows one ZMET2 molecule bridging two nucleosomes within a dinucleosome. We find that the CD stabilizes binding, whereas the BAH domain enables allosteric activation by the H3K9me mark. ZMET2 further couples recognition of H3K9me to an increase in the specificity for hemimethylated versus unmethylated DNA. We propose a model in which synergistic coupling between recognition of nucleosome spacing, H3K9 methylation, and DNA modification allows ZMET2 to maintain DNA methylation in heterochromatin with high fidelity.
History
DepositionSep 19, 2018-
Header (metadata) releaseOct 31, 2018-
Map releaseOct 31, 2018-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9127.png

Downloads & links

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Map

FileDownload / File: emd_9127.map.gz / Format: CCP4 / Size: 3.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationNegative stain map of ZMET2 in complex with H3Kc9me3 dinucleosome with 20 pase pairs of linker DNA.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.14 Å/pix.
x 96 pix.
= 301.44 Å		3.14 Å/pix.
x 96 pix.
= 301.44 Å		3.14 Å/pix.
x 96 pix.
= 301.44 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.04 / Movie #1: 0.04
Minimum - Maximum-0.06780341 - 0.1547642
Average (Standard dev.)0.00025151044 (±0.014551457)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions969696
Spacing969696
CellA=B=C: 301.44 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.143.143.14
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z301.440301.440301.440
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS969696
D min/max/mean-0.0680.1550.000

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Supplemental data

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Sample components

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Entire : Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of...

EntireName: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.
Components
  • Complex: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.
    • Complex: Xenopus histones
    • Complex: ZMET2
    • Complex: 601 dinucleosomal DNA

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Supramolecule #1: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of...

SupramoleculeName: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.
type: complex / ID: 1 / Parent: 0

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Supramolecule #2: Xenopus histones

SupramoleculeName: Xenopus histones / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Xenopus laevis (African clawed frog)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #3: ZMET2

SupramoleculeName: ZMET2 / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Zea mays (maize)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Supramolecule #4: 601 dinucleosomal DNA

SupramoleculeName: 601 dinucleosomal DNA / type: complex / ID: 4 / Parent: 1
Source (natural)Organism: synthetic construct (others)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 8
StainingType: NEGATIVE / Material: Uranyl Formate
GridDetails: unspecified

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Electron microscopy

MicroscopeFEI TECNAI 20
Image recordingFilm or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Average electron dose: 20.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: LAB6
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD

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Image processing

CTF correctionSoftware - Name: Gctf
Startup modelType of model: OTHER / Details: Ab initio model
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 28.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 22000
Initial angle assignmentType: OTHER / Details: See publication.
Final angle assignmentType: OTHER / Details: See publication.

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