[English] 日本語
Yorodumi
- EMDB-43049: Cryo-electron tomogram of mitochondria from cryo-FIB milled l-Opa... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-43049
TitleCryo-electron tomogram of mitochondria from cryo-FIB milled l-Opa1* mouse embryonic fibroblasts
Map data
Sample
  • Cell: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletionMitochondrion
Keywordsmitochondria / cristae / remodeler / fusogen / STRUCTURAL PROTEIN
Biological speciesMus musculus (house mouse)
Methodelectron tomography / cryo EM
AuthorsFry MY / Navarro PP / Ananda VY / Ge Y / McDonald JL / Hakim P / Lugo CM / Luce BE / Chao LH
Funding support United States, Switzerland, 6 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM142553 United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK)DK125263 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)CA248565 United States
Jane Coffin Childs (JCC) Fund United States
Swiss National Science FoundationP2BSP3_188112 Switzerland
Swiss National Science FoundationP400PB_199252 Switzerland
CitationJournal: EMBO J / Year: 2024
Title: In situ architecture of Opa1-dependent mitochondrial cristae remodeling.
Authors: Michelle Y Fry / Paula P Navarro / Pusparanee Hakim / Virly Y Ananda / Xingping Qin / Juan C Landoni / Sneha Rath / Zintis Inde / Camila Makhlouta Lugo / Bridget E Luce / Yifan Ge / Julie L ...Authors: Michelle Y Fry / Paula P Navarro / Pusparanee Hakim / Virly Y Ananda / Xingping Qin / Juan C Landoni / Sneha Rath / Zintis Inde / Camila Makhlouta Lugo / Bridget E Luce / Yifan Ge / Julie L McDonald / Ilzat Ali / Leillani L Ha / Benjamin P Kleinstiver / David C Chan / Kristopher A Sarosiek / Luke H Chao /
Abstract: Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms ...Cristae membrane state plays a central role in regulating mitochondrial function and cellular metabolism. The protein Optic atrophy 1 (Opa1) is an important crista remodeler that exists as two forms in the mitochondrion, a membrane-anchored long form (l-Opa1) and a processed short form (s-Opa1). The mechanisms for how Opa1 influences cristae shape have remained unclear due to lack of native three-dimensional views of cristae. We perform in situ cryo-electron tomography of cryo-focused ion beam milled mouse embryonic fibroblasts with defined Opa1 states to understand how each form of Opa1 influences cristae architecture. In our tomograms, we observe a variety of cristae shapes with distinct trends dependent on s-Opa1:l-Opa1 balance. Increased l-Opa1 levels promote cristae stacking and elongated mitochondria, while increased s-Opa1 levels correlated with irregular cristae packing and round mitochondria shape. Functional assays indicate a role for l-Opa1 in wild-type apoptotic and calcium handling responses, and show a compromised respiratory function under Opa1 imbalance. In summary, we provide three-dimensional visualization of cristae architecture to reveal relationships between mitochondrial ultrastructure and cellular function dependent on Opa1-mediated membrane remodeling.
History
DepositionDec 7, 2023-
Header (metadata) releaseJan 31, 2024-
Map releaseJan 31, 2024-
UpdateFeb 14, 2024-
Current statusFeb 14, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_43049.png

Downloads & links

-
Map

FileDownload / File: emd_43049.map.gz / Format: CCP4 / Size: 315.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 22.06 Å
Density
Minimum - Maximum-32.206435999999997 - 87.248069999999998
Average (Standard dev.)13.352292 (±2.9149015)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-104104-113
Dimensions720511225
Spacing511720225
CellA: 11272.66 Å / B: 15883.199 Å / C: 4963.5 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : mitochondria in mouse embryonic fibroblasts with OMA1 deletion an...

EntireName: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletionMitochondrion
Components
  • Cell: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletionMitochondrion

-
Supramolecule #1: mitochondria in mouse embryonic fibroblasts with OMA1 deletion an...

SupramoleculeName: mitochondria in mouse embryonic fibroblasts with OMA1 deletion and OPA1-exon5b deletion
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 5 / Focused ion beam - Current: 0.01 / Focused ion beam - Duration: 600 / Focused ion beam - Temperature: 88 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 150
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is TFS Aquilos2. This is not in a list of allowed values {'DB235', 'OTHER'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.5 µm / Nominal defocus min: 3.5 µm
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 3.27 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionAlgorithm: BACK PROJECTION / Software - Name: IMOD / Number images used: 46

+
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