[English] 日本語
Yorodumi
- EMDB-0117: Subtomogram averaging of nucleosome particles decorating chromati... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-0117
TitleSubtomogram averaging of nucleosome particles decorating chromatin plates from metaphase chromosomes
Map dataStructure of decorative particles
Sample
  • Complex: Chromatin plates from metaphase chromosomes
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 30.0 Å
AuthorsChicano A / Crosas E / Engel BD / Melero R / Oton J / Daban JR
Funding support Spain, 1 items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2010-18939 Spain
CitationJournal: EMBO J / Year: 2019
Title: Frozen-hydrated chromatin from metaphase chromosomes has an interdigitated multilayer structure.
Authors: Andrea Chicano / Eva Crosas / Joaquín Otón / Roberto Melero / Benjamin D Engel / Joan-Ramon Daban /
Abstract: Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated ...Cryo-electron tomography and small-angle X-ray scattering were used to investigate the chromatin folding in metaphase chromosomes. The tomographic 3D reconstructions show that frozen-hydrated chromatin emanated from chromosomes is planar and forms multilayered plates. The layer thickness was measured accounting for the contrast transfer function fringes at the plate edges, yielding a width of ~ 7.5 nm, which is compatible with the dimensions of a monolayer of nucleosomes slightly tilted with respect to the layer surface. Individual nucleosomes are visible decorating distorted plates, but typical plates are very dense and nucleosomes are not identifiable as individual units, indicating that they are tightly packed. Two layers in contact are ~ 13 nm thick, which is thinner than the sum of two independent layers, suggesting that nucleosomes in the layers interdigitate. X-ray scattering of whole chromosomes shows a main scattering peak at ~ 6 nm, which can be correlated with the distance between layers and between interdigitating nucleosomes interacting through their faces. These observations support a model where compact chromosomes are composed of many chromatin layers stacked along the chromosome axis.
History
DepositionJul 10, 2018-
Header (metadata) releaseAug 1, 2018-
Map releaseJan 16, 2019-
UpdateJan 13, 2021-
Current statusJan 13, 2021Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.135
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.135
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0117.png

Downloads & links

-
Map

FileDownload / File: emd_0117.map.gz / Format: CCP4 / Size: 489.3 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of decorative particles
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
4.21 Å/pix.
x 50 pix.
= 210.5 Å		4.21 Å/pix.
x 50 pix.
= 210.5 Å		4.21 Å/pix.
x 50 pix.
= 210.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.21 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.127 / Movie #1: 0.135
Minimum - Maximum-0.22380047 - 0.29629463
Average (Standard dev.)-4.4945185e-12 (±0.05643651)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions505050
Spacing505050
CellA=B=C: 210.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.214.214.21
M x/y/z505050
origin x/y/z0.0000.0000.000
length x/y/z210.500210.500210.500
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS505050
D min/max/mean-0.2240.296-0.000

-
Supplemental data

-
Sample components

-
Entire : Chromatin plates from metaphase chromosomes

EntireName: Chromatin plates from metaphase chromosomes
Components
  • Complex: Chromatin plates from metaphase chromosomes

-
Supramolecule #1: Chromatin plates from metaphase chromosomes

SupramoleculeName: Chromatin plates from metaphase chromosomes / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 / Details: Nucleosome particles in the plates
Source (natural)Organism: Homo sapiens (human) / Strain: HeLa / Organelle: Metaphase chromosomes

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.2 / Details: 5 mM Pipes (pH 7.2), 5 mM NaCl, and 5 mM MgCl2
VitrificationCryogen name: ETHANE-PROPANE / Instrument: FEI VITROBOT MARK III
DetailsChromatin emanated from soft-denatured metaphase chromosomes

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsPhase plate: VOLTA PHASE PLATE / Energy filter - Name: GIF 2002
Image recording#0 - Image recording ID: 1 / #0 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #0 - Average electron dose: 1.8 e/Å2 / #1 - Image recording ID: 2 / #1 - Film or detector model: GATAN K2 SUMMIT (4k x 4k) / #1 - Average electron dose: 1.8 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated defocus min: 0.5 µm / Calibrated magnification: 33000 / Illumination mode: OTHER / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Image recording ID1
Final reconstructionNumber classes used: 4 / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 30.0 Å / Resolution method: OTHER / Details: MonoRes / Number subtomograms used: 315
ExtractionNumber tomograms: 1 / Number images used: 902 / Reference model: de novo / Method: manually / Software - Name: EMAN2
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: Xmipp (ver. 2.4)

+
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