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- EMDB-70131: KICSTOR-GATOR1 complex (SZT2 [2800-3432], C12orf66) focused refinement -

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Basic information

Entry
Database: EMDB / ID: EMD-70131
TitleKICSTOR-GATOR1 complex (SZT2 [2800-3432], C12orf66) focused refinement
Map dataSharpened final map
Sample
  • Complex: Binary complex of KICSTOR-GATOR1
    • Complex: GATOR1 subcomplex
    • Complex: KICSTOR subcomplex
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: 3.65 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: Cell / Year: 2026
Title: Structure of the lysosomal KICSTOR-GATOR1-SAMTOR nutrient-sensing supercomplex.
Authors: Christopher J Lupton / Charles Bayly-Jones / Shuqi Dong / Terrance Lam / Wentong Luo / Gareth D Jones / Chantel Mastos / Nicholas J Frescher / San S Lim / Alastair C Keen / Luke E Formosa / ...Authors: Christopher J Lupton / Charles Bayly-Jones / Shuqi Dong / Terrance Lam / Wentong Luo / Gareth D Jones / Chantel Mastos / Nicholas J Frescher / San S Lim / Alastair C Keen / Luke E Formosa / Hari Venugopal / Yong-Gang Chang / Michelle L Halls / Andrew M Ellisdon /
Abstract: The guanosine triphosphate (GTP)-bound state of the heterodimeric Rag GTPases functions as a molecular switch regulating mechanistic target of rapamycin complex 1 (mTORC1) activation at the lysosome ...The guanosine triphosphate (GTP)-bound state of the heterodimeric Rag GTPases functions as a molecular switch regulating mechanistic target of rapamycin complex 1 (mTORC1) activation at the lysosome downstream of amino acid fluctuations. Under low amino acid conditions, GTPase-activating protein (GAP) activity toward Rags 1 (GATOR1) promotes RagA GTP hydrolysis, preventing mTORC1 activation. KICSTOR recruits and regulates GATOR1 at the lysosome by undefined mechanisms. Here, we resolve the KICSTOR-GATOR1 structure, revealing a striking ∼60-nm crescent-shaped assembly. GATOR1 anchors to KICSTOR via an extensive interface, and mutations that disrupt this interaction impair mTORC1 regulation. The S-adenosylmethionine sensor SAMTOR binds KICSTOR in a manner incompatible with metabolite binding, providing structural insight into methionine sensing via SAMTOR-KICSTOR association. We discover that KICSTOR and GATOR1 form a dimeric supercomplex. This assembly restricts GATOR1 to an orientation that favors the low-affinity active GAP mode of Rag GTPase engagement while sterically restricting access to the high-affinity inhibitory mode, consistent with a model of an active lysosomal GATOR1 docking complex.
History
DepositionApr 9, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_70131.png

Downloads & links

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Map

FileDownload / File: emd_70131.map.gz / Format: CCP4 / Size: 52.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened final map
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 240 pix.
= 240. Å		1 Å/pix.
x 240 pix.
= 240. Å		1 Å/pix.
x 240 pix.
= 240. 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: 3.0
Minimum - Maximum-0.10231833 - 16.541471000000001
Average (Standard dev.)-0.0015919856 (±0.47413564)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions240240240
Spacing240240240
CellA=B=C: 240.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_70131_msk_1.map
Projections & Slices
AxesZYX

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Histogram

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Additional map: Raw averaged final map

Fileemd_70131_additional_1.map
AnnotationRaw averaged final map
Projections & Slices
AxesZYX

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Half map: Half map 1

Fileemd_70131_half_map_1.map
AnnotationHalf map 1
Projections & Slices
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Histogram

Histogram (log scale)

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Half map: Half map 2

Fileemd_70131_half_map_2.map
AnnotationHalf map 2
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Histogram

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Sample components

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Entire : Binary complex of KICSTOR-GATOR1

EntireName: Binary complex of KICSTOR-GATOR1
Components
  • Complex: Binary complex of KICSTOR-GATOR1
    • Complex: GATOR1 subcomplex
    • Complex: KICSTOR subcomplex

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Supramolecule #1: Binary complex of KICSTOR-GATOR1

SupramoleculeName: Binary complex of KICSTOR-GATOR1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 298 KDa

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Supramolecule #2: GATOR1 subcomplex

SupramoleculeName: GATOR1 subcomplex / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#2, #7
Source (natural)Organism: Homo sapiens (human)

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Supramolecule #3: KICSTOR subcomplex

SupramoleculeName: KICSTOR subcomplex / type: complex / ID: 3 / Parent: 1 / Macromolecule list: #3-#6
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

Concentration0.68 mg/mL
BufferpH: 7.4
GridModel: Quantifoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: HOLEY
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.8 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

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER / Details: Ab initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.65 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 172244
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: FLEXIBLE FIT

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