6ZPN | pdb_00006zpn

Crystal structure of Chaetomium thermophilum Raptor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free: 
    0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work: 
    0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 
    0.229 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 6ZPN

This is version 1.2 of the entry. See complete history

Literature

The dynamic mechanism of 4E-BP1 recognition and phosphorylation by mTORC1.

Bohm, R.Imseng, S.Jakob, R.P.Hall, M.N.Maier, T.Hiller, S.

(2021) Mol Cell 81: 2403

  • DOI: https://doi.org/10.1016/j.molcel.2021.03.031
  • Primary Citation Related Structures: 
    6ZPN

  • PubMed Abstract: 

    The activation of cap-dependent translation in eukaryotes requires multisite, hierarchical phosphorylation of 4E-BP by the 1 MDa kinase mammalian target of rapamycin complex 1 (mTORC1). To resolve the mechanism of this hierarchical phosphorylation at the atomic level, we monitored by NMR spectroscopy the interaction of intrinsically disordered 4E binding protein isoform 1 (4E-BP1) with the mTORC1 subunit regulatory-associated protein of mTOR (Raptor). The N-terminal RAIP motif and the C-terminal TOR signaling (TOS) motif of 4E-BP1 bind separate sites in Raptor, resulting in avidity-based tethering of 4E-BP1. This tethering orients the flexible central region of 4E-BP1 toward the mTORC1 kinase site for phosphorylation. The structural constraints imposed by the two tethering interactions, combined with phosphorylation-induced conformational switching of 4E-BP1, explain the hierarchy of 4E-BP1 phosphorylation by mTORC1. Furthermore, we demonstrate that mTORC1 recognizes both free and eIF4E-bound 4E-BP1, allowing rapid phosphorylation of the entire 4E-BP1 pool and efficient activation of translation. Finally, our findings provide a mechanistic explanation for the differential rapamycin sensitivity of the 4E-BP1 phosphorylation sites.


  • Organizational Affiliation
    • Biozentrum, University of Basel, 4056 Basel, Switzerland.

Macromolecule Content 

  • Total Structure Weight: 339.28 kDa 
  • Atom Count: 17,406 
  • Modeled Residue Count: 2,158 
  • Deposited Residue Count: 3,008 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
WD_REPEATS_REGION domain-containing protein
A, B
1,504Thermochaetoides thermophila DSM 1495Mutation(s): 0 
Gene Names: CTHT_0014610
UniProt
Find proteins for G0S1S2 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S1S2 
Go to UniProtKB:  G0S1S2
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S1S2
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.50 Å
  • R-Value Free:  0.245 (Depositor), 0.244 (DCC) 
  • R-Value Work:  0.228 (Depositor), 0.228 (DCC) 
  • R-Value Observed: 0.229 (Depositor) 
Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 183.306α = 90
b = 183.306β = 90
c = 271.393γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
Cootmodel building
DIALSdata scaling
PHASERphasing
DIALSdata processing
DIALSdata reduction

Structure Validation

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Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Swiss National Science FoundationSwitzerland159696
Swiss National Science FoundationSwitzerland179323

Revision History  (Full details and data files)

  • Version 1.0: 2021-05-19
    Type: Initial release
  • Version 1.1: 2021-06-16
    Changes: Database references
  • Version 1.2: 2024-01-31
    Changes: Data collection, Database references, Refinement description