[English] 日本語
Yorodumi
- EMDB-56112: Cryo-electron tomogram of endosomes in HeLa cells -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-56112
TitleCryo-electron tomogram of endosomes in HeLa cells
Map data
Sample
  • Cell: HeLa cells
Keywordsclathrin / flat clathrin lattice / endosomes / ENDOCYTOSIS
Biological speciesHomo sapiens (human)
Methodelectron tomography / cryo EM
AuthorsHakala M / Moparthi SB / Ganeva I / Gul M / Bernat-Silvestre C / Marcuello C / Espadas J / Colom A / Kudryashev M / Kukulski W ...Hakala M / Moparthi SB / Ganeva I / Gul M / Bernat-Silvestre C / Marcuello C / Espadas J / Colom A / Kudryashev M / Kukulski W / Vassilopoulos S / Kaksonen M / Roux A
Funding support1 items
OrganizationGrant numberCountry
Not funded
CitationJournal: Nat Commun / Year: 2026
Title: Two-dimensional HRS condensates drive the assembly of flat clathrin lattices on endosomes.
Authors: Markku Hakala / Satish Babu Moparthi / Iva Ganeva / Mehmet Gül / César Bernat-Silvestre / Carlos Marcuello / Javier Espadas / Adai Colom / Mikhail Kudryashev / Wanda Kukulski / Stéphane ...Authors: Markku Hakala / Satish Babu Moparthi / Iva Ganeva / Mehmet Gül / César Bernat-Silvestre / Carlos Marcuello / Javier Espadas / Adai Colom / Mikhail Kudryashev / Wanda Kukulski / Stéphane Vassilopoulos / Marko Kaksonen / Aurélien Roux /
Abstract: In cells, the curved clathrin structures in vesicle budding are well characterized, while the flat ones remain poorly understood. Here, we reconstitute the flat assembly of ESCRT-0 protein HRS and ...In cells, the curved clathrin structures in vesicle budding are well characterized, while the flat ones remain poorly understood. Here, we reconstitute the flat assembly of ESCRT-0 protein HRS and clathrin onto lipid membranes in vitro. HRS forms gel-like protein condensates at micromolar concentrations in solutions. These condensates spread as a two-dimensional layer on negatively charged membranes and, together with clathrin, form multilayered coats. Importantly, the two-dimensional condensates spontaneously form only on membranes at HRS concentrations below 50 nM, its cytoplasmic concentration. Correlative cryo-electron tomography of HRS-labelled endosomes in cells reveals a multilayered structure containing a flat clathrin layer 16 nm away from the membrane, consistent with our in vitro findings. Cholesterol enhances HRS recruitment to the membrane both in cells and in supported bilayers. Furthermore, cholesterol promotes the phase separation of HRS onto membranes, which in turn concentrates cholesterol underneath. This positive feedback promotes the formation of HRS-clathrin microdomains that sorts reconstituted ubiquitinated cargoes. Altogether, our results show that the distinct architecture of ESCRT-0 is assembled by the two-dimensional phase-separation of HRS which drives the assembly of flat clathrin coats.
History
DepositionDec 18, 2025-
Header (metadata) releaseMay 20, 2026-
Map releaseMay 20, 2026-
UpdateMay 20, 2026-
Current statusMay 20, 2026Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_56112.png

Downloads & links

-
Map

FileDownload / File: emd_56112.map.gz / Format: CCP4 / Size: 3 GB / Type: IMAGE STORED AS SIGNED BYTE
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5.94 Å/pix.
x 780 pix.
= 4632.42 Å		5.94 Å/pix.
x 2048 pix.
= 12163.072 Å		5.94 Å/pix.
x 2048 pix.
= 12163.072 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: 5.939 Å
Density

Histogram

Histogram (log scale)
Minimum - Maximum-128.0 - 127.0
Average (Standard dev.)18.269012 (±16.065739000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin00-390
Dimensions20482048780
Spacing20482048780
CellA: 12163.072 Å / B: 12163.072 Å / C: 4632.42 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Sample components

-
Entire : HeLa cells

EntireName: HeLa cells
Components
  • Cell: HeLa cells

-
Supramolecule #1: HeLa cells

SupramoleculeName: HeLa cells / type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)

-
Experimental details

-
Structure determination

Methodcryo EM
Processingelectron tomography
Aggregation statecell

-
Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE
SectioningFocused ion beam - Instrument: OTHER / Focused ion beam - Ion: OTHER / Focused ion beam - Voltage: 30 / Focused ion beam - Current: 0.05 / Focused ion beam - Duration: 1500 / Focused ion beam - Temperature: 95 K / Focused ion beam - Initial thickness: 1000 / Focused ion beam - Final thickness: 225
Focused ion beam - Details: The value given for _em_focused_ion_beam.instrument is Aquilos 2 cryo-FIB-SEM. 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: FEI FALCON IV (4k x 4k) / Average electron dose: 1.0 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: 5.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionSoftware - Name: IMOD / Number images used: 121
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION

+
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