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- EMDB-77328: LRRK2 I2020T filaments formed in the presence of MLi-2 -

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Open data


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Basic information

Entry
Database: EMDB / ID: EMD-77328
TitleLRRK2 I2020T filaments formed in the presence of MLi-2
Map dataLRRK2 I2020T filaments formed in the presence of MLi-2
Sample
  • Cell: HEK293T cell expressing human LRRK2 I2020T treated with MLi-2
KeywordsLRRK2 / leucine-rich repeat kinase 2 / Parkinson's disease / microtubule / kinase inhibitor / MLi-2 / cryo-electron tomography / subtomogram averaging / PROTEIN FIBRIL
Biological speciesHomo sapiens (human)
Methodsubtomogram averaging / cryo EM / Resolution: 16.0 Å
AuthorsBasiashvili T / Villa E
Funding support United States, 1 items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP) United States
CitationJournal: To Be Published
Title: Focused map of the WD40:WD40 interaction interface in microtubule-associated LRRK2 I2020T filaments formed in the presence of MLi-2
Authors: Basiashvili T / Villa E
History
DepositionMay 27, 2026-
Header (metadata) releaseAug 5, 2026-
Map releaseAug 5, 2026-
UpdateAug 5, 2026-
Current statusAug 5, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_77328.png

Downloads & links

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Map

FileDownload / File: emd_77328.map.gz / Format: CCP4 / Size: 686.5 KB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLRRK2 I2020T filaments formed in the presence of MLi-2
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
5 Å/pix.
x 56 pix.
= 280. Å		5 Å/pix.
x 56 pix.
= 280. Å		5 Å/pix.
x 56 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 5 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.154
Minimum - Maximum-0.63904893 - 0.77610636
Average (Standard dev.)0.012030537 (±0.13032386)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions565656
Spacing565656
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: Half Map A

Fileemd_77328_half_map_1.map
AnnotationHalf Map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B

Fileemd_77328_half_map_2.map
AnnotationHalf Map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : HEK293T cell expressing human LRRK2 I2020T treated with MLi-2

EntireName: HEK293T cell expressing human LRRK2 I2020T treated with MLi-2
Components
  • Cell: HEK293T cell expressing human LRRK2 I2020T treated with MLi-2

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Supramolecule #1: HEK293T cell expressing human LRRK2 I2020T treated with MLi-2

SupramoleculeName: HEK293T cell expressing human LRRK2 I2020T treated with MLi-2
type: cell / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human) / Strain: Hek293T

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation statecell

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Sample preparation

BufferpH: 7.2
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 3.78 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 5.0 µm / Nominal defocus min: 3.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 16.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1.4) / Number subtomograms used: 21116
ExtractionNumber tomograms: 26 / Number images used: 21116 / Software - Name: Warp
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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