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- EMDB-73491: Focused refinement map on LRRK2 bound to GMPPNP (inactive) -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-73491
TitleFocused refinement map on LRRK2 bound to GMPPNP (inactive)
Map data
Sample
  • Organelle or cellular component: Leucine Rich repeat kinase 2 bound to GMP-PNP
KeywordsKinase / GTPases / HYDROLASE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.35 Å
AuthorsVillagran Suarez A / Bodrug T / Leschziner A
Funding support United States, 1 items
OrganizationGrant numberCountry
Aligning Science Across Parkinsons (ASAP)ASAP-000519 United States
CitationJournal: Cell(Cambridge,Mass.) / Year: 2026
Title: The structural basis for LRRK2's activation and autoinhibition
Authors: Villagran Suarez A / Hatch KS / Bodrug T / Gai W / Surridge KJ / Moussikhina E / Nguyen KH / Sanz-Murillo M / Callahan R / Xiong E / Ramos D / Zhu L / Dederer V / Mathea S / Iwasa J / Knapp ...Authors: Villagran Suarez A / Hatch KS / Bodrug T / Gai W / Surridge KJ / Moussikhina E / Nguyen KH / Sanz-Murillo M / Callahan R / Xiong E / Ramos D / Zhu L / Dederer V / Mathea S / Iwasa J / Knapp S / Shokat KM / Reck-Peterson SL / Leschziner AE
History
DepositionOct 21, 2025-
Header (metadata) releaseAug 19, 2026-
Map releaseAug 19, 2026-
UpdateAug 19, 2026-
Current statusAug 19, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73491.png

Downloads & links

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Map

FileDownload / File: emd_73491.map.gz / Format: CCP4 / Size: 91.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 288 pix.
= 269.28 Å		0.94 Å/pix.
x 288 pix.
= 269.28 Å		0.94 Å/pix.
x 288 pix.
= 269.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.935 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0948
Minimum - Maximum-0.31612992 - 0.4548517
Average (Standard dev.)0.00042125097 (±0.012994049)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions288288288
Spacing288288288
CellA=B=C: 269.28 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_73491_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_73491_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 : Leucine Rich repeat kinase 2 bound to GMP-PNP

EntireName: Leucine Rich repeat kinase 2 bound to GMP-PNP
Components
  • Organelle or cellular component: Leucine Rich repeat kinase 2 bound to GMP-PNP

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Supramolecule #1: Leucine Rich repeat kinase 2 bound to GMP-PNP

SupramoleculeName: Leucine Rich repeat kinase 2 bound to GMP-PNP / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Homo sapiens (human)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Number grids imaged: 1 / Number real images: 7272 / Average electron dose: 56.68 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: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.35 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56741
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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