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- EMDB-30711: Masked wing-a region of TSC complex -

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Basic information

Entry
Database: EMDB / ID: EMD-30711
TitleMasked wing-a region of TSC complex
Map datamasked wing-a region of TSC complex
Sample
  • Complex: Masked wing-a region of TSC complex
Function / homology
Function and homology information


memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of insulin receptor signaling pathway / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / cardiac muscle cell differentiation / cell projection organization ...memory T cell differentiation / TSC1-TSC2 complex binding / TSC1-TSC2 complex / Inhibition of TSC complex formation by PKB / regulation of insulin receptor signaling pathway / cellular response to decreased oxygen levels / negative regulation of cilium assembly / regulation of cell-matrix adhesion / cardiac muscle cell differentiation / cell projection organization / negative regulation of ATP-dependent activity / Energy dependent regulation of mTOR by LKB1-AMPK / response to growth factor / ATPase inhibitor activity / negative regulation of cell size / regulation of stress fiber assembly / activation of GTPase activity / negative regulation of TOR signaling / anoikis / regulation of small GTPase mediated signal transduction / TBC/RABGAPs / AKT phosphorylates targets in the cytosol / protein folding chaperone complex / negative regulation of macroautophagy / Macroautophagy / negative regulation of mitophagy / positive chemotaxis / D-glucose import / Constitutive Signaling by AKT1 E17K in Cancer / negative regulation of Wnt signaling pathway / associative learning / regulation of endocytosis / positive regulation of macroautophagy / positive regulation of focal adhesion assembly / phosphatase binding / vesicle-mediated transport / negative regulation of TORC1 signaling / lipid droplet / myelination / positive regulation of GTPase activity / Hsp70 protein binding / negative regulation of insulin receptor signaling pathway / protein folding chaperone / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / GTPase activator activity / insulin-like growth factor receptor signaling pathway / adult locomotory behavior / hippocampus development / cellular response to starvation / cell-matrix adhesion / positive regulation of protein ubiquitination / negative regulation of protein kinase activity / kidney development / TP53 Regulates Metabolic Genes / phosphatidylinositol 3-kinase/protein kinase B signal transduction / response to insulin / neural tube closure / Hsp90 protein binding / synapse organization / potassium ion transport / cerebral cortex development / small GTPase binding / endocytosis / protein import into nucleus / intracellular protein localization / lamellipodium / protein-folding chaperone binding / heart development / cell cortex / cytoplasmic vesicle / adaptive immune response / lysosome / cell population proliferation / regulation of cell cycle / postsynaptic density / protein stabilization / ciliary basal body / lysosomal membrane / negative regulation of cell population proliferation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / protein-containing complex / nucleus / membrane / 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-like helical / 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: 4.1 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: 0.018
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.018
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_30711.png

Downloads & links

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Map

FileDownload / File: emd_30711.map.gz / Format: CCP4 / Size: 536.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmasked wing-a region of TSC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.36 Å/pix.
x 520 pix.
= 705.12 Å		1.36 Å/pix.
x 520 pix.
= 705.12 Å		1.36 Å/pix.
x 520 pix.
= 705.12 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.356 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.018 / Movie #1: 0.018
Minimum - Maximum-0.054449875 - 0.08774595
Average (Standard dev.)2.0173768e-05 (±0.0006180766)
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-0.0540.0880.000

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Supplemental data

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Sample components

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Entire : Masked wing-a region of TSC complex

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

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

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

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.1 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 131022
Initial angle assignmentType: OTHER
Final angle assignmentType: MAXIMUM LIKELIHOOD

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