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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: To Be Published
Title: The Asgard archaeal ESCRT-III system remodels eukaryotic membranes, shedding light on the emergence of eukaryogenesis
Authors: Melnikov N / Junglas B / Halbi G / Nachmias D / Upcher A / Zalk R / Sachse C / Bernheim-Groswasser A / Elia N
History
DepositionJun 7, 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_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
Brightness
Contrast
Others
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

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

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

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_50583_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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
Startup modelType of model: INSILICO MODEL
Final angle assignmentType: NOT APPLICABLE
FSC plot (resolution estimation)

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