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- EMDB-50583: 360 A Loki CHMP4-7 rods -

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Basic information

Entry
Database: EMDB / ID: EMD-50583
Title360 A Loki CHMP4-7 rods
Map data
Sample
  • Complex: Loki CHMP4-7 rods
    • Protein or peptide: Vps20/32/60-like protein (ESCRT-III)
KeywordsESCRT-III / membrane remodling / tubulation / archaea / Loki / LIPID BINDING PROTEIN
Function / homologySnf7 family / Snf7 / vacuolar transport / Vps20/32/60-like protein (ESCRT-III)
Function and homology information
Biological speciesCandidatus Lokiarchaeia archaeon (archaea)
Methodhelical reconstruction / cryo EM / Resolution: 3.55 Å
AuthorsMelnikov N / Junglas B / Halbi G / Nachmias D / Upcher A / Zalk R / Sachse C / Bernheim-Groswasser A / Elia N
Funding support Israel, 2 items
OrganizationGrant numberCountry
Israel Science Foundation1323/18 Israel
Israel Science Foundation2101/20 Israel
CitationJournal: EMBO J / Year: 2025
Title: The Asgard archaeal ESCRT-III system forms helical filaments and remodels eukaryotic-like membranes.
Authors: Nataly Melnikov / Benedikt Junglas / Gal Halbi / Dikla Nachmias / Erez Zerbib / Noam Gueta / Alexander Upcher / Ran Zalk / Carsten Sachse / Anne Bernheim-Groswasser / Natalie Elia /
Abstract: The ESCRT machinery mediates membrane remodeling in numerous processes in cells including cell division and nuclear membrane reformation. The identification of ESCRT homologs in Asgard archaea, ...The ESCRT machinery mediates membrane remodeling in numerous processes in cells including cell division and nuclear membrane reformation. The identification of ESCRT homologs in Asgard archaea, currently considered the closest prokaryotic relative of eukaryotes, implies a role for ESCRTs in the membrane remodeling processes that occurred during eukaryogenesis. Yet, the function of these distant ESCRT homologs is mostly unresolved. Here we show that Asgard ESCRT-III proteins of the Lokiarcheota self-assemble into helical filaments, a hallmark of the ESCRT system. We determined the cryo-EM structure of the filaments at 3.6 Å resolution and found that they share features of bacterial and eukaryotic ESCRT-III assemblies. Markedly, Asgard ESCRT-III filaments bound and deformed eukaryotic-like membrane vesicles. Oligonucleotides facilitated the assembly of ESCRT-III filaments and tuned the extent of membrane remodeling. The ability of Asgard archaeal ESCRTs to remodel eukaryotic-like membranes, which are fundamentally different from archaeal membranes, and the structural properties of these proteins places them at the junction between prokaryotes and eukaryotes.
History
DepositionJun 7, 2024-
Header (metadata) releaseApr 16, 2025-
Map releaseApr 16, 2025-
UpdateOct 29, 2025-
Current statusOct 29, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_50583.png

Downloads & links

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Map

FileDownload / File: emd_50583.map.gz / Format: CCP4 / Size: 824 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 600 pix.
= 816. Å		1.36 Å/pix.
x 600 pix.
= 816. Å		1.36 Å/pix.
x 600 pix.
= 816. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 1.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.143
Minimum - Maximum-0.29238564 - 0.8220866
Average (Standard dev.)0.0035664917 (±0.027654622)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions600600600
Spacing600600600
CellA=B=C: 816.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_50583_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram (log scale)

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Half map: #2

Fileemd_50583_half_map_2.map
Projections & Slices
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Sample components

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Entire : Loki CHMP4-7 rods

EntireName: Loki CHMP4-7 rods
Components
  • Complex: Loki CHMP4-7 rods
    • Protein or peptide: Vps20/32/60-like protein (ESCRT-III)

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Supramolecule #1: Loki CHMP4-7 rods

SupramoleculeName: Loki CHMP4-7 rods / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Details: Loki CHMP4-7 rods in the presence of CHMP1-3 and DNA
Source (natural)Organism: Candidatus Lokiarchaeia archaeon (archaea) / Strain: KKK44605.1

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Macromolecule #1: Vps20/32/60-like protein (ESCRT-III)

MacromoleculeName: Vps20/32/60-like protein (ESCRT-III) / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Candidatus Lokiarchaeia archaeon (archaea) / Strain: Loki GC14_75
Molecular weightTheoretical: 24.739963 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria)
SequenceString: MGLKKKLFPR KKGKEKANLI TNAKVHIHKL NLVNRNYTKR AEISRKNAKI ALRRGEKTRA KNFLIQYKSY NAKIDRSNNI RSKIERQIQ AIEEGQLISQ TGSIFEGIRD ELKYIATEAS PAKVAEIAED SDVYVSEIEE AADILAGDPE IDLGIDVTDE L NQLETELL ...String:
MGLKKKLFPR KKGKEKANLI TNAKVHIHKL NLVNRNYTKR AEISRKNAKI ALRRGEKTRA KNFLIQYKSY NAKIDRSNNI RSKIERQIQ AIEEGQLISQ TGSIFEGIRD ELKYIATEAS PAKVAEIAED SDVYVSEIEE AADILAGDPE IDLGIDVTDE L NQLETELL LSQGGTMPDA PSDDLQYIPE YGDELEEEVE SKTKEKVQAE IEKLRKELES

UniProtKB: Vps20/32/60-like protein (ESCRT-III)

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.6
Sugar embeddingMaterial: vitrous ice
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 BIOCONTINUUM (6k x 4k) / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Helical parameters - Δz: 1.05 Å
Applied symmetry - Helical parameters - Δ&Phi: 173.9 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 228688
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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