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

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 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.
SampleComplex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.:
Xenopus histones / ZMET2 / 601 dinucleosomal DNA
SourceXenopus laevis (African clawed frog) / Zea mays (maize) / synthetic construct (others)
Methodsingle particle reconstruction / 28 Å resolution
AuthorsStoddard CI / Feng S / Campbell MG / Liu W / Wang H / Zhong X / Bernatavichute Y / Cheng Y / Jacobsen SE / Narlikar GJ
CitationJournal: To Be Published
Title: A nucleosome bridging mechanism for activation of a maintenance DNA methyltransferase
Authors: Stoddard CI / Feng S / Campbell MG / Liu W / Wang H / Zhong X / Bernatavichute Y / Cheng Y / Jacobsen SE / Narlikar GJ
DateDeposition: Sep 19, 2018 / Header (metadata) release: Oct 31, 2018 / Map release: Oct 31, 2018 / Last update: Oct 31, 2018

-
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

Downloads & links

-
Map

Fileemd_9127.map.gz (map file in CCP4 format, 3539 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
96 pix
3.14 Å/pix.
= 301.44 Å
96 pix
3.14 Å/pix.
= 301.44 Å
96 pix
3.14 Å/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
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.06780341 - 0.1547642
Average (Standard dev.)0.00025151044 (0.014551457)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions969696
Origin0.00.00.0
Limit95.095.095.0
Spacing969696
CellA=B=C: 301.44 Å
α=β=γ: 90.0 deg.

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
start NX/NY/NZ
NX/NY/NZ
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.
Number of components: 4

-
Component #1: protein, Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base...

ProteinName: Complex of ZMET2 with H3Kc9me3 dinucleosome with 20 base pairs of linker DNA.
Recombinant expression: No

-
Component #2: protein, Xenopus histones

ProteinName: Xenopus histones / Recombinant expression: No
SourceSpecies: Xenopus laevis (African clawed frog)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #3: protein, ZMET2

ProteinName: ZMET2 / Recombinant expression: No
SourceSpecies: Zea mays (maize)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Component #4: protein, 601 dinucleosomal DNA

ProteinName: 601 dinucleosomal DNA / Recombinant expression: No
SourceSpecies: synthetic construct (others)
Source (engineered)Expression System: Escherichia coli (E. coli)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: particle
Sample solutionpH: 8
Support filmunspecified
VitrificationCryogen name: NONE

-
Electron microscopy imaging

ImagingMicroscope: FEI TECNAI 20
Electron gunElectron source: LAB6 / Accelerating voltage: 200 kV / Electron dose: 2 e/Å2 / Illumination mode: OTHER
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

-
Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 22000
3D reconstructionSoftware: RELION / Resolution: 28 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: See publication.

+
About Yorodumi

-
News

-
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. See below links for details.
  • 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

-
Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

+
Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

+
Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

+
Apr 13, 2016. Omokage search got faster

Omokage search got faster

  • The computation time became ~1/2 compared to the previous version by re-optimization of data accession
  • Enjoy "shape similarity" of biomolecules, more!

Related info.: Omokage search

Read more

-
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.

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