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- PDB-25gf: Cryo-EM structure of the human KPTN-ITFG2-C12orf66-SZT2(2189-3432... -

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Basic information

Entry
Database: PDB / ID: 25gf
TitleCryo-EM structure of the human KPTN-ITFG2-C12orf66-SZT2(2189-3432) complex
Components
  • KICSTOR complex protein ITFG2
  • KICSTOR complex protein SZT2
  • KICSTOR complex protein kaptin
  • KICSTOR subunit 2
KeywordsSIGNALING PROTEIN / Complex / lysosome / mTORC1
Function / homology
Function and homology information


KICSTOR complex / regulation of superoxide dismutase activity / corpus callosum morphogenesis / protein localization to lysosome / Amino acids regulate mTORC1 / stereocilium / post-embryonic development / postsynaptic actin cytoskeleton / regulation of TOR signaling / cellular response to glucose starvation ...KICSTOR complex / regulation of superoxide dismutase activity / corpus callosum morphogenesis / protein localization to lysosome / Amino acids regulate mTORC1 / stereocilium / post-embryonic development / postsynaptic actin cytoskeleton / regulation of TOR signaling / cellular response to glucose starvation / negative regulation of TORC1 signaling / cellular response to amino acid starvation / actin filament organization / central nervous system development / actin filament binding / peroxisome / lamellipodium / lysosomal membrane / glutamatergic synapse / nucleoplasm / cytosol
Similarity search - Function
KICSTOR subunit 2 / KICSTOR complex protein C12orf66-like, central domain superfamily / KICSTOR complex C12orf66 like / Kaptin / Integrin-alpha FG-GAP repeat-containing protein 2 / Integrin-alpha FG-GAP repeat-containing protein 2 / Protein SZT2 / Integrin alpha, N-terminal / WD40-repeat-containing domain superfamily
Similarity search - Domain/homology
KICSTOR complex protein SZT2 / KICSTOR complex protein ITFG2 / KICSTOR subunit 2 / KICSTOR complex protein kaptin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.81 Å
AuthorsYang, A. / Liang, L.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32571452 China
CitationJournal: To Be Published
Title: Mechanistic insights into GATOR1 inhibition by GATOR2 and KICSTOR
Authors: Yang, A. / Liang, L.
History
DepositionApr 1, 2026Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: KICSTOR complex protein kaptin
D: KICSTOR subunit 2
B: KICSTOR complex protein ITFG2
C: KICSTOR complex protein SZT2


Theoretical massNumber of molelcules
Total (without water)285,9874
Polymers285,9874
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein KICSTOR complex protein kaptin / Actin-associated protein 2E4


Mass: 48185.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPTN / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9Y664
#2: Protein KICSTOR subunit 2 / KICSTOR complex protein C12orf66


Mass: 50469.758 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KICS2, C12orf66 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q96MD2
#3: Protein KICSTOR complex protein ITFG2 / Integrin-alpha FG-GAP repeat-containing protein 2


Mass: 49365.742 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITFG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q969R8
#4: Protein KICSTOR complex protein SZT2 / Seizure threshold 2 protein homolog


Mass: 137966.250 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SZT2, C1orf84, KIAA0467 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q5T011
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Complex of the human KPTN-ITFG2-C12orf66-SZT2(2189-3432)
Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
SpecimenConc.: 0.9 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameVersionCategoryDetails (eV)
1Topazparticle selection
2PHENIX1.20.1_4487model refinement
13cryoSPARC3D reconstruction3Dflex
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.81 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51000 / Symmetry type: POINT
RefinementHighest resolution: 3.81 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00617898
ELECTRON MICROSCOPYf_angle_d1.12424284
ELECTRON MICROSCOPYf_dihedral_angle_d7.3382373
ELECTRON MICROSCOPYf_chiral_restr0.0522694
ELECTRON MICROSCOPYf_plane_restr0.0063141

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