[English] 日本語
Yorodumi
- EMDB-72321: Structure of ATP synthase monomer from mouse embryonic fibroblasts -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-72321
TitleStructure of ATP synthase monomer from mouse embryonic fibroblasts
Map datafiltsharp map of ATP synthase monomer from mouse embryonic fibroblasts output from M
Sample
  • Complex: ATP synthase monomer from mouse embryonic fibroblasts
KeywordsATP synthase / mitochondria / MEMBRANE PROTEIN
Biological speciesMus musculus (house mouse)
Methodsubtomogram averaging / cryo EM / Resolution: 12.9 Å
AuthorsMedina M / Chang Y / Rahmani H / Fuentes D / Barad BA / Grotjahn DA
Funding support United States, 6 items
OrganizationGrant numberCountry
Damon Runyon Cancer Research FoundationDRR-65-21 United States
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)RF1NS125674 United States
National Institutes of Health/Office of the DirectorS10OD032467 United States
Other privateThe Pew Scholars Program
Other privateARCS (Achievement rewards for college scientists)
Other privateCollins Medical Trust
CitationJournal: bioRxiv / Year: 2025
Title: Surface morphometrics reveals local membrane thickness variation in organellar subcompartments.
Authors: Michaela Medina / Ya-Ting Chang / Hamidreza Rahmani / Daniel Fuentes / Benjamin A Barad / Danielle A Grotjahn /
Abstract: Lipid bilayers form the basis of organellar architecture, structure, and compartmentalization in the cell. Decades of biophysical, biochemical, and imaging studies on purified or reconstituted ...Lipid bilayers form the basis of organellar architecture, structure, and compartmentalization in the cell. Decades of biophysical, biochemical, and imaging studies on purified or reconstituted liposomes have shown that variations in lipid composition influence the physical properties of membranes, such as thickness and curvature. However, similar studies characterizing these membrane properties within the native cellular context have remained technically challenging. Recent advancements in cellular cryo-electron tomography (cryo-ET) imaging enable high-resolution, three-dimensional views of native organellar membrane architecture preserved in near-native conditions. We previously developed a 'Surface Morphometrics' pipeline that generates surface mesh reconstructions to model and quantify cellular membrane ultrastructure from cryo-ET data. Here, we expand this pipeline to measure the distance between the phospholipid head groups (PHG) of the membrane bilayer as a readout of membrane thickness. Using this approach, we demonstrate thickness variations both within and between distinct organellar membranes. We also demonstrate that membrane thickness positively correlates with other features, such as membrane curvedness. Further, we show that subcompartments of the mitochondrial inner membrane exhibit varying membrane thicknesses that are independent of network morphology (i.e., fragmented versus elongated networks). Finally, we demonstrate that large membrane-associated macromolecular complexes exhibit distinct density profiles that correlate with local variations in membrane thickness. Overall, our updated Surface Morphometrics pipeline provides a framework for investigating how changes in membrane composition in various cellular and disease contexts affect organelle ultrastructure and function.
History
DepositionAug 25, 2025-
Header (metadata) releaseSep 10, 2025-
Map releaseSep 10, 2025-
UpdateJan 14, 2026-
Current statusJan 14, 2026Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_72321.png

Downloads & links

-
Map

FileDownload / File: emd_72321.map.gz / Format: CCP4 / Size: 3.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationfiltsharp map of ATP synthase monomer from mouse embryonic fibroblasts output from M
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.32 Å/pix.
x 100 pix.
= 332. Å		3.32 Å/pix.
x 100 pix.
= 332. Å		3.32 Å/pix.
x 100 pix.
= 332. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.32 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.70285463 - 1.2510879
Average (Standard dev.)0.018990016 (±0.13864064)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions100100100
Spacing100100100
CellA=B=C: 332.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Half map: half map output from M

Fileemd_72321_half_map_1.map
Annotationhalf map output from M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map output from M

Fileemd_72321_half_map_2.map
Annotationhalf map output from M
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : ATP synthase monomer from mouse embryonic fibroblasts

EntireName: ATP synthase monomer from mouse embryonic fibroblasts
Components
  • Complex: ATP synthase monomer from mouse embryonic fibroblasts

-
Supramolecule #1: ATP synthase monomer from mouse embryonic fibroblasts

SupramoleculeName: ATP synthase monomer from mouse embryonic fibroblasts / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Mus musculus (house mouse)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

-
Sample preparation

BufferpH: 7
GridModel: Quantifoil R1/4 / Material: GOLD / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
Details: fibronectin-treated (500 ug/ml, Corning) and UV sterilized
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 100 % / Chamber temperature: 310.15 K / Instrument: FEI VITROBOT MARK IV
DetailsCells were frozen and then thinned using Aquilos2 for FIB-milling

-
Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Digitization - Dimensions - Width: 5760 pixel / Digitization - Dimensions - Height: 4092 pixel / Average electron dose: 3.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 8.0 µm / Nominal defocus min: 4.0 µm / Nominal magnification: 53000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 12.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Software - details: M was used for post-processing / Number subtomograms used: 8993
ExtractionNumber tomograms: 42 / Number images used: 8993 / Software - Name: I3 / Software - details: Manual dipole selection
CTF correctionType: NONE
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 4.0) / Software - details: Relion + M
FSC plot (resolution estimation)

+
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