5EF5 | pdb_00005ef5

Crystal structure of Chaetomium thermophilum Raptor

• PDB DOI: https://doi.org/10.2210/pdb5EF5/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Thermochaetoides thermophila
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 4.30 Å
• R-Value Free: 
  0.391 (Depositor), 0.396 (DCC) 
• R-Value Work: 
  0.371 (Depositor), 0.378 (DCC) 
• R-Value Observed: 
  0.372 (Depositor) 

Literature

Architecture of human mTOR complex 1.

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

(2016) Science 351: 48-52

• PubMed: 26678875 
• DOI: https://doi.org/10.1126/science.aaa3870
• Primary Citation 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.
Biozentrum, University of Basel, Basel, Switzerland.
Biozentrum, University of Basel, Basel, Switzerland. [e-mail] [e-mail] [e-mail].
Institute of Molecular Biology and Biophysics, ETH Zürich, Zürich, Switzerland. [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 175.18 kDa 
• Atom Count: 10,164 
• Modeled Residue Count: 2,033 
• Deposited Residue Count: 2,058 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Raptor from Chaetomium thermophilum	A [auth E], B [auth A]	1,029	Thermochaetoides thermophila	Mutation(s): 0  Gene Names: Raptor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 4.30 Å
• R-Value Free:  0.391 (Depositor), 0.396 (DCC) 
• R-Value Work:  0.371 (Depositor), 0.378 (DCC) 
• R-Value Observed: 0.372 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 183.83	α = 90
b = 183.83	β = 90
c = 272.9	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
SHELXCD	phasing
PHASER	phasing
O	model building
Coot	model building

Structure Validation

Currently 5EF5 does not have a validation slider image.

Entry History 

Deposition Data

• Released Date: 2015-12-30 
Deposition Author(s): Imseng, S., Sauer, E., Aylett, C.H.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: 2019-04-24
  Changes: Data collection, Source and taxonomy
• Version 1.3: 2019-10-02
  Changes: Data collection, Derived calculations
• Version 1.4: 2024-05-08
  Changes: Database references