[English] 日本語
Yorodumi
- EMDB-52543: Cryo-ET tomogram #5 of thylakoids inside spinach chloroplast (top... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-52543
TitleCryo-ET tomogram #5 of thylakoids inside spinach chloroplast (top view on the membranes)
Map dataCryo-electron tomogram of thylakoids within spinach chloroplast (top view on the membranes)
Sample
  • Organelle or cellular component: Chloroplast
Keywordschloroplast / spinach / thylakoids / plastoglobules / PHOTOSYNTHESIS
Biological speciesSpinacia oleracea (spinach)
Methodelectron tomography / cryo EM
AuthorsWietrzynski W / Lamm L / Engel BD
Funding support France, 1 items
OrganizationGrant numberCountry
Human Frontier Science Program (HFSP)RGP0005/2021 France
Citation
Journal: Elife / Year: 2025
Title: Molecular architecture of thylakoid membranes within intact spinach chloroplasts.
Authors: Wojciech Wietrzynski / Lorenz Lamm / William H J Wood / Matina-Jasemi Loukeri / Lorna Malone / Tingying Peng / Matthew P Johnson / Benjamin D Engel /
Abstract: Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling the architecture of an elaborate membrane network to the spatial organization of individual ...Thylakoid membranes coordinate the light reactions of photosynthesis across multiple scales, coupling the architecture of an elaborate membrane network to the spatial organization of individual protein complexes embedded within this network. Previously, we used in situ cryo-electron tomography (cryo-ET) to reveal the native thylakoid architecture of the green alga (Engel et al., 2015) and then map the molecular organization of these thylakoids with single-molecule precision (Wietrzynski et al., 2020). However, it remains to be shown how generalizable this green algal blueprint is to the thylakoids of vascular plants, which possess distinct membrane architecture subdivided into grana stacks interconnected by non-stacked stromal lamellae. Here, we continue our cryo-ET investigation to reveal the molecular architecture of thylakoids within intact chloroplasts isolated from spinach (). We visualize the fine ultrastructural details of grana membranes, as well as interactions between thylakoids and plastoglobules. We apply AI-based computational approaches (Lamm et al., 2024) to quantify the organization of photosynthetic complexes within the plane of the thylakoid membrane and across adjacent stacked membranes. Our analysis reveals that the molecular organization of thylakoid membranes in vascular plants and green algae is strikingly similar. We find that PSII organization is non-crystalline and has uniform concentration both within the membrane plane and across stacked grana membranes. Similar to , we observe strict lateral heterogeneity of PSII and PSI at the boundary between appressed and non-appressed thylakoid domains, with no evidence for a distinct grana margin region where these complexes have been proposed to intermix. Based on these measurements, we support a simple two-domain model for the molecular organization of thylakoid membranes in both green algae and plants.
#1: Journal: Elife / Year: 2025
Title: Molecular architecture of thylakoid membranes within intact spinach chloroplasts
Authors: Wietrzynski W / Lamm L / Wood WH / Loukeri MJ / Malone L / Peng T / Johnson MP / Engel BD
History
DepositionJan 14, 2025-
Header (metadata) releaseFeb 26, 2025-
Map releaseFeb 26, 2025-
UpdateSep 24, 2025-
Current statusSep 24, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_52543.png

Downloads & links

-
Map

FileDownload / File: emd_52543.map.gz / Format: CCP4 / Size: 1.5 GB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-electron tomogram of thylakoids within spinach chloroplast (top view on the membranes)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
14.08 Å/pix.
x 464 pix.
= 6533.12 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 Å		14.08 Å/pix.
x 928 pix.
= 13066.24 Å

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 14.08 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-60.272762 - 50.607939999999999
Average (Standard dev.)0.0050308616 (±0.93169093)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions928928464
Spacing928928464
CellA: 13066.24 Å / B: 13066.24 Å / C: 6533.12 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : Chloroplast

EntireName: Chloroplast
Components
  • Organelle or cellular component: Chloroplast

-
Supramolecule #1: Chloroplast

SupramoleculeName: Chloroplast / type: organelle_or_cellular_component / ID: 1 / Parent: 0
Details: Isolated chloroplast of Spinach (Spinacia oleracea) visualised by cryo-ET
Source (natural)Organism: Spinacia oleracea (spinach) / Organ: leaf / Organelle: chloroplast

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.2
Details: 0.45 M Sorbitol, 20 mM Tricine-KOH, 10 mM EDTA, 10 mM NaHCO3, 5 mM MgCl2, 0.1% BSA, 0.2% D-Ascorbate
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE-PROPANE / Chamber humidity: 75 % / Chamber temperature: 295 K / Instrument: FEI VITROBOT MARK IV
Cryo protectantno cryoprotectant
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.1 / Focused ion beam - Duration: 1800 / Focused ion beam - Temperature: 77 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 120
Focused ion beam - Details: Clumps of chloroplast were milled in a step-wise manner according to the routine protocols.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is ...Focused ion beam - Details: Clumps of chloroplast were milled in a step-wise manner according to the routine protocols.. The value given for _em_focused_ion_beam.instrument is TFS Aquilos. This is not in a list of allowed values {'OTHER', 'DB235'} so OTHER is written into the XML file.

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 120.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 2.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 60
CTF correctionType: NONE

+
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