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- PDB-9v80: Cryo-EM structure of KICSTOR CCC complex (state 4) -

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Basic information

Entry
Database: PDB / ID: 9v80
TitleCryo-EM structure of KICSTOR CCC complex (state 4)
Components
  • KICSTOR complex protein ITFG2
  • KICSTOR complex protein SZT2
  • KICSTOR complex protein kaptin
KeywordsSIGNALING PROTEIN / lipid binding protein
Function / homology
Function and homology information


regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation ...regulation of superoxide dismutase activity / KICSTOR complex / corpus callosum morphogenesis / germinal center B cell differentiation / protein localization to lysosome / regulation of TOR signaling / Amino acids regulate mTORC1 / postsynaptic actin cytoskeleton / stereocilium / pigmentation / cellular response to glucose starvation / negative regulation of TORC1 signaling / cellular response to amino acid starvation / actin filament organization / central nervous system development / post-embryonic development / actin filament binding / peroxisome / lamellipodium / lysosomal membrane / intracellular membrane-bounded organelle / glutamatergic synapse / Golgi apparatus / nucleoplasm / cytosol
Similarity search - Function
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 complex protein kaptin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.95 Å
AuthorsSu, M.-Y.
Funding support China, 1items
OrganizationGrant numberCountry
Other government20231120103446003 China
CitationJournal: To Be Published
Title: Cryo-EM structure of KICSTOR CCC complex
Authors: Su, M.-Y.
History
DepositionMay 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Primary map / Data content type: Primary map / 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 SZT2
B: KICSTOR complex protein ITFG2
C: KICSTOR complex protein kaptin


Theoretical massNumber of molelcules
Total (without water)475,9473
Polymers475,9473
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 SZT2 / Seizure threshold 2 protein homolog


Mass: 378453.438 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: Homo sapiens (human) / References: UniProt: Q5T011
#2: 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: Homo sapiens (human) / References: UniProt: Q969R8
#3: Protein KICSTOR complex protein kaptin / Actin-associated protein 2E4


Mass: 48128.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: KPTN / Production host: Homo sapiens (human) / References: UniProt: Q9Y664
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: KICSTOR CCC complex / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.28 MDa / Experimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Homo sapiens (human)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 57.65 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.95 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 271421 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0049803
ELECTRON MICROSCOPYf_angle_d0.66213352
ELECTRON MICROSCOPYf_dihedral_angle_d6.9641392
ELECTRON MICROSCOPYf_chiral_restr0.0431560
ELECTRON MICROSCOPYf_plane_restr0.0051724

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