cryo-EM structure of mTORC1 bound to PRAS40-fused active RagA/C GTPases
ELECTRON MICROSCOPY
Refinement
RMS Deviations
Key
Refinement Restraint Deviation
r_mcangle_it
60.216
r_scbond_it
45.948
r_mcbond_it
36.707
r_dihedral_angle_2_deg
33.536
r_dihedral_angle_3_deg
18.235
r_dihedral_angle_4_deg
15.747
r_dihedral_angle_1_deg
6.426
r_angle_refined_deg
1.879
r_chiral_restr
0.132
r_bond_refined_d
0.009
RMS Deviations
Key
Refinement Restraint Deviation
r_mcangle_it
60.216
r_scbond_it
45.948
r_mcbond_it
36.707
r_dihedral_angle_2_deg
33.536
r_dihedral_angle_3_deg
18.235
r_dihedral_angle_4_deg
15.747
r_dihedral_angle_1_deg
6.426
r_angle_refined_deg
1.879
r_chiral_restr
0.132
r_bond_refined_d
0.009
r_gen_planes_refined
0.009
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Sample
cryoEM structure of mTORC1 bound to RagA/C complex
Sample Components
mTORC1
RagA/C
Specimen Preparation
Sample Aggregation State
PARTICLE
Vitrification Instrument
FEI VITROBOT MARK III
Cryogen Name
ETHANE
Sample Vitrification Details
3D Reconstruction
Reconstruction Method
SINGLE PARTICLE
Number of Particles
90809
Reported Resolution (Å)
5.5
Resolution Method
FSC 0.143 CUT-OFF
Other Details
For the final reconstruction of mTORC1-RagA/C structure we used a strategy taking advantage of the relion particle symmetry expand program, and duplic ...
For the final reconstruction of mTORC1-RagA/C structure we used a strategy taking advantage of the relion particle symmetry expand program, and duplicated the C2-refined particles and applied the appropriate rotation and translation to generate a set of monomers. We performed mTORC1-RagA/C 'pseudo-monomer' focussed classification with signal subtraction and obtained a reconstruction of 5.5 A resolution map. This cryo-EM density corresponded to the mTORC1-RagA/C pseudomonomer, where the previously published structure for apo-mTORC1 (PDB ID 6BCX) and our high-resolution crystal structure of RagA/C (6S6A) were fitted with great confidence from our experimental analysis including Pulldown assays, mutational at per-residue level in the binding interface and HDX-Mass Spectrometry.
Refinement Type
Symmetry Type
POINT
Point Symmetry
C1
Map-Model Fitting and Refinement
Id
1 (6BCX, 6S6A)
Refinement Space
REAL
Refinement Protocol
RIGID BODY FIT
Refinement Target
Overall B Value
283
Fitting Procedure
Details
Cryo-EM model of mTORC1-RagA/C was refined using REFMAC5 program in CCPEM package, with a composite map of the 3D reconstruction of mTORC1-RagA/C pseu ...
Cryo-EM model of mTORC1-RagA/C was refined using REFMAC5 program in CCPEM package, with a composite map of the 3D reconstruction of mTORC1-RagA/C pseudo-monomer (as mentioned in Reconstruction section) of one protomer together with the generated map for the other second protomer of mTORC1-RagA/C. This second protomer of mTORC1-RagA/C map was generated by simply aligning the first 3D reconstructed pseudomonomer map onto the mTORC1 dimer consensus C2 map and then obtained the rotation-translation matrix with CHIMERA and then used Maputils program in CCP4i. From the resulting mTORC1-RagA/C dimer map, the model of mTORC1-RagA/C was built by using previously published structure of apo-mTORC1 (PDB ID 6BCX) and our crystal structure of RagA/C was fitted (PDB ID 6S6A, unreleased). The entire mTORC1-RagA/C final model was refined using REFMAC5 program using the restraints from the crystal structure of RagA/C and previously published mTORC1 structure. Side chains were removed before refinement, since these were not evident in the cryo-EM densities. Separate model refinements were performed against single half-maps, and the resulting models were compared with the other half-maps to confirm the absence of overfitting.
