National Institutes of Health/National Human Genome Research Institute
EY012287
United States
Spanish Ministry of Science, Innovation, and Universities
BFU2016-75984
Spain
Citation
Journal: Nat Commun / Year: 2019 Title: Structural and functional analysis of the role of the chaperonin CCT in mTOR complex assembly. Authors: Jorge Cuéllar / W Grant Ludlam / Nicole C Tensmeyer / Takuma Aoba / Madhura Dhavale / César Santiago / M Teresa Bueno-Carrasco / Michael J Mann / Rebecca L Plimpton / Aman Makaju / Sarah ...Authors: Jorge Cuéllar / W Grant Ludlam / Nicole C Tensmeyer / Takuma Aoba / Madhura Dhavale / César Santiago / M Teresa Bueno-Carrasco / Michael J Mann / Rebecca L Plimpton / Aman Makaju / Sarah Franklin / Barry M Willardson / José M Valpuesta / Abstract: The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two ...The mechanistic target of rapamycin (mTOR) kinase forms two multi-protein signaling complexes, mTORC1 and mTORC2, which are master regulators of cell growth, metabolism, survival and autophagy. Two of the subunits of these complexes are mLST8 and Raptor, β-propeller proteins that stabilize the mTOR kinase and recruit substrates, respectively. Here we report that the eukaryotic chaperonin CCT plays a key role in mTORC assembly and signaling by folding both mLST8 and Raptor. A high resolution (4.0 Å) cryo-EM structure of the human mLST8-CCT intermediate isolated directly from cells shows mLST8 in a near-native state bound to CCT deep within the folding chamber between the two CCT rings, and interacting mainly with the disordered N- and C-termini of specific CCT subunits of both rings. These findings describe a unique function of CCT in mTORC assembly and a distinct binding site in CCT for mLST8, far from those found for similar β-propeller proteins.
History
Deposition
Dec 27, 2018
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Header (metadata) release
Jul 3, 2019
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Map release
Jul 3, 2019
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Update
Nov 6, 2019
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Current status
Nov 6, 2019
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Download / File: emd_4503.map.gz / Format: CCP4 / Size: 83.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation
Human substrate-free CCT
Voxel size
X=Y=Z: 0.89 Å
Density
Contour Level
By AUTHOR: 0.0038 / Movie #1: 0.0038
Minimum - Maximum
-0.008884804 - 0.021280224
Average (Standard dev.)
-0.00028310472 (±0.0029267685)
Symmetry
Space group: 1
Details
EMDB XML:
Map geometry
Axis order
X
Y
Z
Origin
0
0
0
Dimensions
280
280
280
Spacing
280
280
280
Cell
A=B=C: 249.2 Å α=β=γ: 90.0 °
CCP4 map header:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.89
0.89
0.89
M x/y/z
280
280
280
origin x/y/z
0.000
0.000
0.000
length x/y/z
249.200
249.200
249.200
α/β/γ
90.000
90.000
90.000
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
280
280
280
D min/max/mean
-0.009
0.021
-0.000
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Supplemental data
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Sample components
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Entire : Human substrate-free CCT
Entire
Name: Human substrate-free CCT
Components
Complex: Human substrate-free CCT
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Supramolecule #1: Human substrate-free CCT
Supramolecule
Name: Human substrate-free CCT / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#8 Details: we have characterized the eukaryotic chaperonin CCT (1 MDa; formed by two copies of eight homologous subunits)
Source (natural)
Organism: Homo sapiens (human)
Recombinant expression
Organism: Homo sapiens (human) / Recombinant cell: HEK293T
Molecular weight
Experimental: 1 MDa
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Concentration
0.5 mg/mL
Buffer
pH: 7.5
Grid
Model: Quantifoil R2/2 / Material: COPPER/RHODIUM / Mesh: 400 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE
Vitrification
Cryogen name: ETHANE
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Electron microscopy
Microscope
FEI TITAN KRIOS
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Number grids imaged: 1 / Number real images: 3292 / Average exposure time: 8.0 sec. / Average electron dose: 42.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
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Image processing
Particle selection
Number selected: 504060
CTF correction
Software - Name: CTFFIND (ver. 4)
Startup model
Type of model: INSILICO MODEL / In silico model: ransac (Xmipp3) and Initial model (Eman2)
Initial angle assignment
Type: COMMON LINE / Software - Name: RELION (ver. 2)
Final 3D classification
Software - Name: RELION (ver. 2)
Final angle assignment
Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 2)
Final reconstruction
Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 2) / Number images used: 139819
FSC plot (resolution estimation)
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Atomic model buiding 1
Refinement
Space: REAL / Protocol: FLEXIBLE FIT
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