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- EMDB-72379: DEPDC5 NPRL2 NPRL3 SZT2 focused refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-72379
TitleDEPDC5 NPRL2 NPRL3 SZT2 focused refinement
Map dataEMReady sharpened map
Sample
  • Complex: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
KeywordsLysosome / GATOR1 / KICSTOR / cell growth / amino acid sensing / mTOR / KPTN / ITFG2 / C12orf66 / SZT2 / NPRL2 / NPRL3 / DEPDC5 / CELL CYCLE
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsBayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
Funding support Australia, 4 items
OrganizationGrant numberCountry
National Health and Medical Research Council (NHMRC, Australia)APP2036864 Australia
Australian Research Council (ARC)DE240100992 Australia
Other governmentMCRF21036 Australia
Australian Research Council (ARC)LE170100016 Australia
CitationJournal: To Be Published
Title: Structure of the lysosomal KICSTOR-GATOR1 nutrient-sensing supercomplex
Authors: Bayly-Jones C / Lupton CJ / Chang YG / Ellisdon AM
History
DepositionAug 28, 2025-
Header (metadata) releaseFeb 11, 2026-
Map releaseFeb 11, 2026-
UpdateFeb 11, 2026-
Current statusFeb 11, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72379.png

Downloads & links

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Map

FileDownload / File: emd_72379.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationEMReady sharpened map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å		1 Å/pix.
x 280 pix.
= 280. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-0.1217913 - 12.354385000000001
Average (Standard dev.)0.058060586 (±0.5346973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin181149162
Dimensions280280280
Spacing280280280
CellA=B=C: 280.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72379_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Raw unsharpened map

Fileemd_72379_additional_1.map
AnnotationRaw unsharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_72379_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_72379_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 : Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KI...

EntireName: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
Components
  • Complex: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex

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Supramolecule #1: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KI...

SupramoleculeName: Dimeric tandem DEPDC5-DEPDC5 interface component of the GATOR1-KICSTOR supercomplex
type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 550 KDa

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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: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 356922
CTF correctionSoftware - Name: CTFFIND / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 356922
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION / Software - details: SpIsoNet refinement
Final 3D classificationSoftware - Name: RELION
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

9o5e


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT

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