[English] 日本語
Yorodumi
- EMDB-50748: Asgard ESCRT-IIIB filament structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-50748
TitleAsgard ESCRT-IIIB filament structure
Map dataPostprocessed map of the Asgard ESCRT-IIIB filament
Sample
  • Organelle or cellular component: Four-protofilament helical structure of Asgard ESCRT-IIIB
    • Protein or peptide: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
KeywordsESCRT-III / filament / membrane binding protein / membrane remodelling / Asgard archaea / MEMBRANE PROTEIN
Function / homologySnf7 family / Snf7 / late endosome to vacuole transport via multivesicular body sorting pathway / vesicle budding from membrane / endomembrane system / cytoplasmic side of plasma membrane / intracellular membrane-bounded organelle / Uncharacterized protein
Function and homology information
Biological speciesCandidatus Heimdallarchaeota archaeon (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsChaaban S / Souza DP / Baum B
Funding support United Kingdom, 2 items
OrganizationGrant numberCountry
Wellcome Trust203276/Z/16/Z United Kingdom
Wellcome Trust210711/Z/18/Z United Kingdom
CitationJournal: Sci Adv / Year: 2025
Title: Asgard archaea reveal the conserved principles of ESCRT-III membrane remodeling.
Authors: Diorge P Souza / Javier Espadas / Sami Chaaban / Edmund R R Moody / Tomoyuki Hatano / Mohan Balasubramanian / Tom A Williams / Aurélien Roux / Buzz Baum /
Abstract: ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis, we ...ESCRT-III proteins assemble into composite polymers that undergo stepwise changes in composition and structure to deform membranes across the tree of life. Here, using a phylogenetic analysis, we demonstrate that the two endosomal sorting complex required for transport III (ESCRT-III) proteins present in eukaryote's closest Asgard archaeal relatives are evolutionarily related to the B- and A-type eukaryotic paralogs that initiate and execute membrane remodeling, respectively. We show that Asgard ESCRT-IIIB assembles into parallel arrays on planar membranes to initiate membrane deformation, from where it recruits ESCRT-IIIA to generate composite polymers. Last, we show that Asgard ESCRT-IIIA is able to remodel membranes into tubes as a likely prelude to scission. Together, these data reveal a set of conserved principles governing ESCRT-III-dependent membrane remodeling that first emerged in a two-component ESCRT-III system in archaea.
History
DepositionJun 24, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateApr 16, 2025-
Current statusApr 16, 2025Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_50748.png

Downloads & links

-
Map

FileDownload / File: emd_50748.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of the Asgard ESCRT-IIIB filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 500 pix.
= 413. Å		0.83 Å/pix.
x 500 pix.
= 413. Å		0.83 Å/pix.
x 500 pix.
= 413. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.826 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.00518
Minimum - Maximum-0.019235931 - 0.042970277
Average (Standard dev.)0.00002761466 (±0.0006114673)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions500500500
Spacing500500500
CellA=B=C: 413.0 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_50748_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unprocessed map of the Asgard ESCRT-IIIB filament

Fileemd_50748_additional_1.map
AnnotationUnprocessed map of the Asgard ESCRT-IIIB filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 1 of the Asgard ESCRT-IIIB filament

Fileemd_50748_half_map_1.map
AnnotationHalf-map 1 of the Asgard ESCRT-IIIB filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: Half-map 2 of the Asgard ESCRT-IIIB filament

Fileemd_50748_half_map_2.map
AnnotationHalf-map 2 of the Asgard ESCRT-IIIB filament
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Four-protofilament helical structure of Asgard ESCRT-IIIB

EntireName: Four-protofilament helical structure of Asgard ESCRT-IIIB
Components
  • Organelle or cellular component: Four-protofilament helical structure of Asgard ESCRT-IIIB
    • Protein or peptide: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

-
Supramolecule #1: Four-protofilament helical structure of Asgard ESCRT-IIIB

SupramoleculeName: Four-protofilament helical structure of Asgard ESCRT-IIIB
type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 3.140 kDa/nm

-
Macromolecule #1: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

MacromoleculeName: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 24.130268 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MVKNWLFGKK RKEDADALAT LKGQQNRLQA EARNLERQSD EQKILASKML KAGNKAGARQ ALKRRAVFMK RLNTVHNTAM NLQAQIDSI QTATSTAETV KAMELGTKVV GEKIKTVSPE RTERVMDSVM EQRDQIEMMT EALSDPSLSE GILDFEDDAA I DEQLAQLE ...String:
MVKNWLFGKK RKEDADALAT LKGQQNRLQA EARNLERQSD EQKILASKML KAGNKAGARQ ALKRRAVFMK RLNTVHNTAM NLQAQIDSI QTATSTAETV KAMELGTKVV GEKIKTVSPE RTERVMDSVM EQRDQIEMMT EALSDPSLSE GILDFEDDAA I DEQLAQLE AEMDLGTTTS LPDVSGLPST PVGTGEKEED TSELEAELEG LKKKMSEDKQ

UniProtKB: Uncharacterized protein

-
Experimental details

-
Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

-
Sample preparation

Concentration0.5 mg/mL
BufferpH: 6 / Component - Concentration: 20.0 mM / Component - Formula: Bis-Tris-HCl / Component - Name: Bis-Tris-HCl
Details: 20 mM Bis-Tris-HCl pH 6.0, 0.12 mM 1,2-dioleoyl-sn-glycero-3-phosphocholine, 0.08 mM 1,2-dioleoyl-sn-glycero-3-phospho-L-serine
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 12 sec.
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 293.15 K / Instrument: FEI VITROBOT MARK IV

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 29600 / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 15.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -178.5 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 274671
Startup modelType of model: NONE / Details: Ab initio
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5)

-
Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: in silico model / Details: ModelAngelo
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

PDB-9ftl:
Asgard ESCRT-IIIB filament structure

+
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