5FVM | pdb_00005fvm

Cryo electron microscopy of a complex of Tor and Lst8

• PDB DOI: https://doi.org/10.2210/pdb5FVM/pdb
• EM Map EMD-3329: EMDB EMDataResource

• Classification: TRANSFERASE
• Organism(s): Kluyveromyces marxianus
• Expression System: Kluyveromyces marxianus
• Mutation(s): No 


• Deposited: 2016-02-09 Released: 2016-04-20 
• Deposition Author(s): Baretic, D., Berndt, A., Ohashi, Y., Johnson, C.M., Williams, R.L.

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Starting Model: experimental

Literature

Tor Forms a Dimer Through an N-Terminal Helical Solenoid with a Complex Topology

Baretic, D., Berndt, A., Ohashi, Y., Johnson, C.M., Williams, R.L.

(2016) Nat Commun 7: 11016

• PubMed: 27072897 
• DOI: https://doi.org/10.1038/ncomms11016
• Primary Citation Related Structures: 
  5FVM


• PubMed Abstract: 
  

  The target of rapamycin (Tor) is a Ser/Thr protein kinase that regulates a range of anabolic and catabolic processes. Tor is present in two complexes, TORC1 and TORC2, in which the Tor-Lst8 heterodimer forms a common sub-complex. We have determined the cryo-electron microscopy (EM) structure of Tor bound to Lst8. Two Tor-Lst8 heterodimers assemble further into a dyad-symmetry dimer mediated by Tor-Tor interactions. The first 1,300 residues of Tor form a HEAT repeat-containing α-solenoid with four distinct segments: a highly curved 800-residue N-terminal 'spiral', followed by a 400-residue low-curvature 'bridge' and an extended 'railing' running along the bridge leading to the 'cap' that links to FAT region. This complex topology was verified by domain insertions and offers a new interpretation of the mTORC1 structure. The spiral of one TOR interacts with the bridge of another, which together form a joint platform for the Regulatory Associated Protein of TOR (RAPTOR) regulatory subunit.

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Organizational Affiliation: 
• MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 626.72 kDa 
• Atom Count: 23,974 
• Modeled Residue Count: 4,832 
• Deposited Residue Count: 5,548 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERINE/THREONINE-PROTEIN KINASE TOR2	A, B	2,471	Kluyveromyces marxianus	Mutation(s): 0  Gene Names: KMAR_30040

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
TARGET OF RAPAMYCIN COMPLEX SUBUNIT LST8	C, D	303	Kluyveromyces marxianus	Mutation(s): 0  Gene Names: KMAR_20458

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.70 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-04-20 
Deposition Author(s): Baretic, D., Berndt, A., Ohashi, Y., Johnson, C.M., Williams, R.L.

Revision History  

• Version 1.0: 2016-04-20
  Type: Initial release
  
• Version 1.1: 2016-04-27
  Changes: Database references
• Version 1.2: 2017-08-02
  Changes: Data collection, Refinement description
• Version 1.3: 2019-10-23
  Changes: Data collection, Other
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references, Refinement description