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- PDB-9fn1: 360 A Loki CHMP4-7 rods -

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Basic information

Entry
Database: PDB / ID: 9fn1
Title360 A Loki CHMP4-7 rods
ComponentsVps20/32/60-like protein (ESCRT-III)
KeywordsLIPID BINDING PROTEIN / ESCRT-III / membrane remodling / tubulation / archaea / Loki
Function / homologySnf7 family / Snf7 / vacuolar transport / Vps20/32/60-like protein (ESCRT-III)
Function and homology information
Biological speciesCandidatus Lokiarchaeia archaeon (archaea)
MethodELECTRON MICROSCOPY / helical 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, 2items
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, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 16, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 16, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
U: Vps20/32/60-like protein (ESCRT-III)


Theoretical massNumber of molelcules
Total (without water)24,7401
Polymers24,7401
Non-polymers00
Water00
1
U: Vps20/32/60-like protein (ESCRT-III)
x 60


Theoretical massNumber of molelcules
Total (without water)1,484,39860
Polymers1,484,39860
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59

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Components

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


Mass: 24739.963 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Candidatus Lokiarchaeia archaeon (archaea)
Strain: Loki GC14_75 / Gene: Lokiarch_16760 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A0F8W953
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: Loki CHMP4-7 rods / Type: COMPLEX
Details: Loki CHMP4-7 rods in the presence of CHMP1-3 and DNA
Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Candidatus Lokiarchaeia archaeon (archaea) / Strain: KKK44605.1
Source (recombinant)Organism: Escherichia coli (E. coli) / Strain: BL21
Buffer solutionpH: 7.6
SpecimenEmbedding applied: YES / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
EM embeddingMaterial: vitrous ice
VitrificationCryogen name: ETHANE

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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: 3000 nm / Nominal defocus min: 1500 nm
Image recordingElectron dose: 30 e/Å2 / Film or detector model: GATAN K3 BIOCONTINUUM (6k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Helical symmertyAngular rotation/subunit: 173.9 ° / Axial rise/subunit: 1.05 Å / Axial symmetry: C1
3D reconstructionResolution: 3.55 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 228688 / Symmetry type: HELICAL
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00775660
ELECTRON MICROSCOPYf_angle_d0.908101760
ELECTRON MICROSCOPYf_dihedral_angle_d15.17829520
ELECTRON MICROSCOPYf_chiral_restr0.05411820
ELECTRON MICROSCOPYf_plane_restr0.02913380

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