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- PDB-9ftm: Asgard ESCRT-IIIB membrane-bound protofilament structure -

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Basic information

Entry
Database: PDB / ID: 9ftm
TitleAsgard ESCRT-IIIB membrane-bound protofilament structure
ComponentsHeimdallarchaeota archaeon AB_125 ESCRT-IIIB
KeywordsMEMBRANE PROTEIN / ESCRT-III / filament / membrane binding protein / membrane remodeling / 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: 6.5 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
G: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
A: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
H: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
I: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
K: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
F: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
B: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB


Theoretical massNumber of molelcules
Total (without water)193,0428
Polymers193,0428
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: Protein
Heimdallarchaeota archaeon AB_125 ESCRT-IIIB / Snf7 domain-containing protein


Mass: 24130.268 Da / Num. of mol.: 8
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

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Experimental details

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Experiment

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

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Sample preparation

ComponentName: Membrane-bound Asgard ESCRT-IIIB protofilament array / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: NATURAL
Molecular weightValue: 33 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

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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

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Processing

EM software
IDNameVersionCategory
2EPUimage acquisition
4CTFFIND4CTF correction
7Coot0.9.3model fitting
9cryoSPARC4.2.1initial Euler assignment
10RELION5final Euler assignment
12RELION53D reconstruction
13PHENIX1.2model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 0.4 ° / Axial rise/subunit: 29.9 Å / Axial symmetry: C1
3D reconstructionResolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 27747 / Symmetry type: HELICAL
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingDetails: The initial model was obtained from the high resolution four-protofilament structure off membranes
Source name: Other / Type: experimental model

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