[English] 日本語
Yorodumi
- EMDB-4483: Correlative FM and ET of GFP-Bax in HeLa cells -

+
Open data


ID or keywords:

Loading...

no data

-
Basic information

Entry
Database: EMDB / ID: 4483
TitleCorrelative FM and ET of GFP-Bax in HeLa cells
Map dataReconstructed tomogram of mitochondria in HeLa cells overexpressing GFP-Bax.
SampleHeLa (homo sapiens):
SourceHomo sapiens (human)
Methodelectron tomography / negative staining
AuthorsAder NR / Hoffmann PC / Ganeva I / Borgeaud AC / Wang C / Youle RJ / Kukulski W
CitationJournal: Elife / Year: 2019
Title: Molecular and topological reorganizations in mitochondrial architecture interplay during Bax-mediated steps of apoptosis.
Authors: Nicholas R Ader / Patrick C Hoffmann / Iva Ganeva / Alicia C Borgeaud / Chunxin Wang / Richard J Youle / Wanda Kukulski
Abstract: During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing ...During apoptosis, Bcl-2 proteins such as Bax and Bak mediate the release of pro-apoptotic proteins from the mitochondria by clustering on the outer mitochondrial membrane and thereby permeabilizing it. However, it remains unclear how outer membrane openings form. Here, we combined different correlative microscopy and electron cryo-tomography approaches to visualize the effects of Bax activity on mitochondria in human cells. Our data show that Bax clusters localize near outer membrane ruptures of highly variable size. Bax clusters contain structural elements suggesting a higher order organization of their components. Furthermore, unfolding of inner membrane cristae is coupled to changes in the supramolecular assembly of ATP synthases, particularly pronounced at membrane segments exposed to the cytosol by ruptures. Based on our results, we propose a comprehensive model in which molecular reorganizations of the inner membrane and sequestration of outer membrane components into Bax clusters interplay in the formation of outer membrane ruptures.
Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).
DateDeposition: Dec 19, 2018 / Header (metadata) release: Feb 13, 2019 / Map release: Feb 13, 2019 / Last update: Feb 13, 2019

-
Structure visualization

Movie
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
  • Solid view (volume rendering)
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Supplemental images

Downloads & links

-
Map

Fileemd_4483.map.gz (map file in CCP4 format, 1342178 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
11.02 Å/pix.
= 1763.2 Å
2048 pix
11.02 Å/pix.
= 22568.961 Å
2048 pix
11.02 Å/pix.
= 22568.961 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 11.02 Å
Density
Minimum - Maximum-535.0 - 885.0
Average (Standard dev.)416.35205000000002 (23.344325999999999)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions20482048160
Origin0.00.0-80.0
Limit2047.02047.079.0
Spacing20482048160
CellA: 22568.96 Å / B: 22568.96 Å / C: 1763.2001 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Integer*27
Å/pix. X/Y/Z11.02000048828111.02000048828111.02
M x/y/z20482048160
origin x/y/z0.0000.0000.000
length x/y/z22568.96122568.9611763.200
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS00-80
NC/NR/NS20482048160
D min/max/mean-535.000885.000416.352

-
Supplemental data

-
Sample components

-
Entire HeLa (homo sapiens)

EntireName: HeLa (homo sapiens)
Details: Cryofixation of cell was performed 16 h after transfection of GFP-Bax plasmid.
Number of components: 1

-
Component #1: cellular-component, HeLa (homo sapiens)

Cellular-componentName: HeLa (homo sapiens)
Details: Cryofixation of cell was performed 16 h after transfection of GFP-Bax plasmid.
Recombinant expression: No
SourceSpecies: Homo sapiens (human)

-
Experimental details

-
Sample preparation

SpecimenSpecimen state: cell / Method: negative staining
Sample solutionpH: 8.4
Staining0.008% uranyl acetate in acetone
VitrificationCryogen name: NONE

-
Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20
Details: ET was done in STEM mode on an axial brightfield detector with a high-tilt tomography holder (Model 2020; Fischione Instruments) at a 1.1nm pixel size with a camera length of 200 mm.
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 1 e/Å2 / Illumination mode: SPOT SCAN
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: OTHER

-
Image acquisition

Image acquisitionDetails: ET was done in STEM mode on an axial brightfield detector with a high-tilt tomography holder (Model 2020; Fischione Instruments) at a 1.1nm pixel size with a camera length of 200 mm. [NOTE: Electron dose unknown. Value specified here is a dummy]

-
Image processing

ProcessingMethod: electron tomography / Number of sections: 237
3D reconstructionAlgorithm: BACK PROJECTION / Software: eTomo / Details: 237 tilted images used from two axies

+
About Yorodumi

-
News

-
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. (see PDBe EMDB page)
  • 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 at PDBe / 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. 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

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