[English] 日本語
Yorodumi
- PDB-9ftl: Asgard ESCRT-IIIB filament structure -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9ftl
TitleAsgard ESCRT-IIIB filament structure
ComponentsHeimdallarchaeota archaeon AB_125 ESCRT-IIIB
KeywordsMEMBRANE PROTEIN / ESCRT-III / filament / membrane binding protein / membrane remodelling / Asgard archaea
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)
MethodELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 2.91 Å
AuthorsChaaban, S. / Souza, D.P. / Baum, B.
Funding support United Kingdom, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB


Theoretical massNumber of molelcules
Total (without water)48,2612
Polymers48,2612
Non-polymers00
Water00
1
A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
a: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB


Theoretical massNumber of molelcules
Total (without water)772,16932
Polymers772,16932
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation15
identity operation1_555x,y,z1

-
Components

#1: Protein Heimdallarchaeota archaeon AB_125 ESCRT-IIIB


Mass: 24130.268 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Heimdallarchaeota archaeon (archaea)
Gene: HeimAB125_14020 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1Q9PC98
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: FILAMENT / 3D reconstruction method: helical reconstruction

-
Sample preparation

ComponentName: Four-protofilament helical structure of Asgard ESCRT-IIIB
Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 3.140 kDa/nm / Experimental value: NO
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Buffer solutionpH: 6
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
Buffer componentConc.: 20 mM / Name: Bis-Tris-HCl / Formula: Bis-Tris-HCl
SpecimenConc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 293.15 K

-
Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of real images: 29600

-
Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.9.3model fitting
9RELION4initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: -178.5 ° / Axial rise/subunit: 15.4 Å / Axial symmetry: C1
3D reconstructionResolution: 2.91 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 274671 / Algorithm: BACK PROJECTION / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: ModelAngelo / Source name: Other / Type: in silico model

+
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