5FLC

Architecture of human mTOR Complex 1 - 5.9 Angstrom reconstruction

• PDB DOI: https://doi.org/10.2210/pdb5FLC/pdb
• EM Map EMD-3213: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Homo sapiens, Spodoptera frugiperda
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2015-10-23 Released: 2015-12-30 
• Deposition Author(s): Aylett, C.H.S., Sauer, E., Imseng, S., Boehringer, D., Hall, M.N., Ban, N., Maier, T.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Architecture of Human Mtor Complex 1

Aylett, C.H.S., Sauer, E., Imseng, S., Boehringer, D., Hall, M.N., Ban, N., Maier, T.

(2016) Science 351: 48

• PubMed: 26678875 
• DOI: https://doi.org/10.1126/science.aaa3870
• Primary Citation of Related Structures:  
  5EF5, 5FLC


• PubMed Abstract: 
  

  Target of rapamycin (TOR), a conserved protein kinase and central controller of cell growth, functions in two structurally and functionally distinct complexes: TORC1 and TORC2. Dysregulation of mammalian TOR (mTOR) signaling is implicated in pathologies that include diabetes, cancer, and neurodegeneration. We resolved the architecture of human mTORC1 (mTOR with subunits Raptor and mLST8) bound to FK506 binding protein (FKBP)-rapamycin, by combining cryo-electron microscopy at 5.9 angstrom resolution with crystallographic studies of Chaetomium thermophilum Raptor at 4.3 angstrom resolution. The structure explains how FKBP-rapamycin and architectural elements of mTORC1 limit access to the recessed active site. Consistent with a role in substrate recognition and delivery, the conserved amino-terminal domain of Raptor is juxtaposed to the kinase active site.

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Organizational Affiliation: 

Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 12-mer - A2B2C2D2E2F2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 702.03 kDa 
• Atom Count: 47,536 
• Modelled Residue Count: 6,966 
• Deposited Residue Count: 7,220 
• Unique protein chains: 6

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE MTOR	A [auth 1], C [auth 3]	615	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE MTOR	B [auth 2], D [auth 4]	365	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
REGULATORY-ASSOCIATED PROTEIN OF MTOR	E [auth A], I [auth E]	1,029	Homo sapiens	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE MTOR	F [auth B], J [auth F]	1,168	Homo sapiens	Mutation(s): 0  EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P42345 (Homo sapiens) Explore P42345  Go to UniProtKB:  P42345
PHAROS:  P42345 GTEx:  ENSG00000198793

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
FKBP	G [auth C], K [auth G]	107	Spodoptera frugiperda	Mutation(s): 0

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8	H [auth D], L [auth H]	326	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVC4 (Homo sapiens) Explore Q9BVC4  Go to UniProtKB:  Q9BVC4
PHAROS:  Q9BVC4 GTEx:  ENSG00000167965

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RAP	M [auth C], N [auth G]	RAPAMYCIN IMMUNOSUPPRESSANT DRUG C51 H79 N O13 QFJCIRLUMZQUOT-HPLJOQBZSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RAP	BindingDB:  5FLC	Kd: 0.6 (nM) from 1 assay(s)
		IC50: min: 0.05, max: 430 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 5.90 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	1.3

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Aylett, C.H.S., Sauer, E., Imseng, S., Boehringer, D., Hall, M.N., Ban, N., Maier, T.

Revision History  

• Version 1.0: 2015-12-30
  Type: Initial release
  
• Version 1.1: 2016-01-13
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Data collection
• Version 1.3: 2019-04-24
  Changes: Data collection, Source and taxonomy