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- EMDB-50749: Asgard ESCRT-IIIB membrane-bound protofilament structure -

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Basic information

Entry
Database: EMDB / ID: EMD-50749
TitleAsgard ESCRT-IIIB membrane-bound protofilament structure
Map dataPostprocessed map of membrane-decorated Asgard ESCRT-IIIB
Sample
  • Organelle or cellular component: Membrane-bound Asgard ESCRT-IIIB protofilament array
    • Protein or peptide: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB
KeywordsESCRT-III / filament / membrane binding protein / membrane remodeling / 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: 6.5 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

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Structure visualization

Supplemental images

emd_50749.png

Downloads & links

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Map

FileDownload / File: emd_50749.map.gz / Format: CCP4 / Size: 78.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPostprocessed map of membrane-decorated Asgard ESCRT-IIIB
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.51 Å/pix.
x 274 pix.
= 413. Å		1.51 Å/pix.
x 274 pix.
= 413. Å		1.51 Å/pix.
x 274 pix.
= 413. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.5073 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0145
Minimum - Maximum-0.031205043 - 0.07789781
Average (Standard dev.)0.00012566037 (±0.001778213)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions274274274
Spacing274274274
CellA=B=C: 413.0002 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_50749_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Unprocessed map membrane-decorated Asgard ESCRT-IIIB

Fileemd_50749_additional_1.map
AnnotationUnprocessed map membrane-decorated Asgard ESCRT-IIIB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 1 of membrane-decorated Asgard ESCRT-IIIB

Fileemd_50749_half_map_1.map
AnnotationHalf-map 1 of membrane-decorated Asgard ESCRT-IIIB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half-map 2 of membrane-decorated Asgard ESCRT-IIIB

Fileemd_50749_half_map_2.map
AnnotationHalf-map 2 of membrane-decorated Asgard ESCRT-IIIB
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Membrane-bound Asgard ESCRT-IIIB protofilament array

EntireName: Membrane-bound Asgard ESCRT-IIIB protofilament array
Components
  • Organelle or cellular component: Membrane-bound Asgard ESCRT-IIIB protofilament array
    • Protein or peptide: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

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Supramolecule #1: Membrane-bound Asgard ESCRT-IIIB protofilament array

SupramoleculeName: Membrane-bound Asgard ESCRT-IIIB protofilament array / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Candidatus Heimdallarchaeota archaeon (archaea)
Molecular weightTheoretical: 33 kDa/nm

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Macromolecule #1: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB

MacromoleculeName: Heimdallarchaeota archaeon AB_125 ESCRT-IIIB / type: protein_or_peptide / ID: 1 / Number of copies: 8 / 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

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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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

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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

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 29.9 Å
Applied symmetry - Helical parameters - Δ&Phi: 0.4 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 5) / Number images used: 27747
Startup modelType of model: NONE / Details: Ab initio
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 5)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: experimental model
Details: The initial model was obtained from the high resolution four-protofilament structure off membranes
RefinementSpace: REAL / Protocol: FLEXIBLE FIT
Output model

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

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