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- EMDB-72380: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map -

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Basic information

Entry
Database: EMDB / ID: EMD-72380
TitleConstitutive dimer GATOR1:SZT2 [1-1330] consensus map
Map dataRaw unsharpened map, consensus from global refinement
Sample
  • Complex: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map
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: 4.2 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) releaseJul 8, 2026-
Map releaseJul 8, 2026-
UpdateJul 8, 2026-
Current statusJul 8, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_72380.png

Downloads & links

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Map

FileReleased
AnnotationRaw unsharpened map, consensus from global refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.44 Å/pix.
x 400 pix.
= 574. Å		1.44 Å/pix.
x 400 pix.
= 574. Å		1.44 Å/pix.
x 400 pix.
= 574. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.435 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.01
Minimum - Maximum-0.02164679 - 0.06050028
Average (Standard dev.)-0.0001705136 (±0.0015498679)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions400400400
Spacing400400400
CellA=B=C: 574.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_72380_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map B

Fileemd_72380_half_map_1.map
AnnotationHalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half map A

Fileemd_72380_half_map_2.map
AnnotationHalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Constitutive dimer GATOR1:SZT2 [1-1330] consensus map

EntireName: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map
Components
  • Complex: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map

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Supramolecule #1: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map

SupramoleculeName: Constitutive dimer GATOR1:SZT2 [1-1330] consensus map / 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: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 28288
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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