[English] 日本語
Yorodumi
- EMDB-9127: A nucleosome bridging mechanism for activation of a maintenance D... -

+
Open data


ID or keywords:

Loading...

-
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

-
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
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_9127.png

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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)

-
Supramolecule #3: ZMET2

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

-
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)

-
Experimental details

-
Structure determination

Methodnegative staining
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
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.

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more