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- EMDB-30710: Masked wing-b region of TSC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30710
TitleMasked wing-b region of TSC complex
Map datamasked wing-b region of TSC complex
Sample
  • Complex: Masked wing-b region of TSC complex
Function / homology
Function and homology information


memory T cell differentiation / : / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of phosphoprotein phosphatase activity / cellular response to decreased oxygen levels / regulation of insulin receptor signaling pathway / : / negative regulation of cilium assembly / regulation of cell-matrix adhesion ...memory T cell differentiation / : / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of phosphoprotein phosphatase activity / cellular response to decreased oxygen levels / regulation of insulin receptor signaling pathway / : / negative regulation of cilium assembly / regulation of cell-matrix adhesion / ATPase inhibitor activity / cardiac muscle cell differentiation / Energy dependent regulation of mTOR by LKB1-AMPK / cell projection organization / negative regulation of ATP-dependent activity / negative regulation of cell size / response to growth factor / regulation of stress fiber assembly / activation of GTPase activity / protein folding chaperone complex / anoikis / negative regulation of TOR signaling / TBC/RABGAPs / negative regulation of mitophagy / regulation of small GTPase mediated signal transduction / AKT phosphorylates targets in the cytosol / negative regulation of macroautophagy / Macroautophagy / negative regulation of Wnt signaling pathway / positive chemotaxis / glucose import / Constitutive Signaling by AKT1 E17K in Cancer / positive regulation of focal adhesion assembly / associative learning / positive regulation of macroautophagy / regulation of endocytosis / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / phosphatase binding / vesicle-mediated transport / negative regulation of TORC1 signaling / Hsp70 protein binding / cellular response to starvation / myelination / viral process / negative regulation of insulin receptor signaling pathway / lipid droplet / GTPase activator activity / adult locomotory behavior / cell-matrix adhesion / insulin-like growth factor receptor signaling pathway / ciliary basal body / phosphatidylinositol 3-kinase/protein kinase B signal transduction / kidney development / positive regulation of protein ubiquitination / neural tube closure / hippocampus development / TP53 Regulates Metabolic Genes / synapse organization / negative regulation of protein kinase activity / Hsp90 protein binding / response to insulin / protein localization / potassium ion transport / cerebral cortex development / small GTPase binding / positive regulation of GTPase activity / endocytosis / protein import into nucleus / lamellipodium / regulation of translation / heart development / cell cortex / protein-folding chaperone binding / cytoplasmic vesicle / adaptive immune response / cell population proliferation / postsynaptic density / lysosome / negative regulation of translation / protein stabilization / regulation of cell cycle / lysosomal membrane / negative regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / membrane / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Tuberin / Tuberin-type domain / Tuberin, N-terminal / Tuberin/Ral GTPase-activating protein subunit alpha / Tuberin / Domain of unknown function (DUF3384) / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 ...Tuberin / Tuberin-type domain / Tuberin, N-terminal / Tuberin/Ral GTPase-activating protein subunit alpha / Tuberin / Domain of unknown function (DUF3384) / Rap/Ran-GAP domain / Rap/Ran-GAP superfamily / TBC1 domain family member 7 / TBC1 domain family member 7, domain 2 / Rap/ran-GAP / Rap GTPase activating proteins domain profile. / Hamartin / Hamartin protein / Rab-GTPase-TBC domain / Rab-GTPase-TBC domain superfamily / Rab-GTPase-TBC domain / TBC/rab GAP domain profile. / Armadillo-type fold
Similarity search - Domain/homology
Tuberin / Hamartin / TBC1 domain family member 7
Similarity search - Component
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.85 Å
AuthorsYang H / Yu Z / Chen X / Li J / Li N / Cheng J / Gao N / Yuan H / Ye D / Guan K / Xu Y
CitationJournal: Nat Commun / Year: 2021
Title: Structural insights into TSC complex assembly and GAP activity on Rheb.
Authors: Huirong Yang / Zishuo Yu / Xizi Chen / Jiabei Li / Ningning Li / Jiaxuan Cheng / Ning Gao / Hai-Xin Yuan / Dan Ye / Kun-Liang Guan / Yanhui Xu /
Abstract: Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small ...Tuberous sclerosis complex (TSC) integrates upstream stimuli and regulates cell growth by controlling the activity of mTORC1. TSC complex functions as a GTPase-activating protein (GAP) towards small GTPase Rheb and inhibits Rheb-mediated activation of mTORC1. Mutations in TSC genes cause tuberous sclerosis. In this study, the near-atomic resolution structure of human TSC complex reveals an arch-shaped architecture, with a 2:2:1 stoichiometry of TSC1, TSC2, and TBC1D7. This asymmetric complex consists of two interweaved TSC1 coiled-coil and one TBC1D7 that spans over the tail-to-tail TSC2 dimer. The two TSC2 GAP domains are symmetrically cradled within the core module formed by TSC2 dimerization domain and central coiled-coil of TSC1. Structural and biochemical analyses reveal TSC2 GAP-Rheb complimentary interactions and suggest a catalytic mechanism, by which an asparagine thumb (N1643) stabilizes γ-phosphate of GTP and accelerate GTP hydrolysis of Rheb. Our study reveals mechanisms of TSC complex assembly and GAP activity.
History
DepositionNov 26, 2020-
Header (metadata) releaseDec 16, 2020-
Map releaseDec 16, 2020-
UpdateJan 27, 2021-
Current statusJan 27, 2021Processing site: PDBj / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by cylindrical radius
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30710.png

Downloads & links

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Map

FileDownload / File: emd_30710.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked wing-b region of TSC complex
Voxel sizeX=Y=Z: 1.356 Å
Density
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.060355853 - 0.12720169
Average (Standard dev.)-7.859195e-06 (±0.0015559003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions520520520
Spacing520520520
CellA=B=C: 705.12 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3561.3561.356
M x/y/z520520520
origin x/y/z0.0000.0000.000
length x/y/z705.120705.120705.120
α/β/γ90.00090.00090.000
start NX/NY/NZ-225-225-225
NX/NY/NZ450450450
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS520520520
D min/max/mean-0.0600.127-0.000

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Supplemental data

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Sample components

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Entire : Masked wing-b region of TSC complex

EntireName: Masked wing-b region of TSC complex
Components
  • Complex: Masked wing-b region of TSC complex

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Supramolecule #1: Masked wing-b region of TSC complex

SupramoleculeName: Masked wing-b region of TSC complex / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Homo sapiens (human)
Recombinant expressionOrganism: 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

BufferpH: 7.4
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 50.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.85 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131022

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