5T0N

Pseudo-apo structure of Sestrin2 at 3.0 angstrom resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The apo-structure of the leucine sensor Sestrin2 is still elusive.

Saxton, R.A.Knockenhauer, K.E.Schwartz, T.U.Sabatini, D.M.

(2016) Sci.Signal. 9: ra92-ra92

  • DOI: 10.1126/scisignal.aah4497

  • PubMed Abstract: 
  • Sestrin2 is a GATOR2-interacting protein that directly binds leucine and is required for the inhibition of mTORC1 under leucine deprivation, indicating that it is a leucine sensor for the mTORC1 pathway. We recently reported the structure of Sestrin2 ...

    Sestrin2 is a GATOR2-interacting protein that directly binds leucine and is required for the inhibition of mTORC1 under leucine deprivation, indicating that it is a leucine sensor for the mTORC1 pathway. We recently reported the structure of Sestrin2 in complex with leucine [Protein Data Bank (PDB) ID, 5DJ4] and demonstrated that mutations in the leucine-binding pocket that alter the affinity of Sestrin2 for leucine result in a corresponding change in the leucine sensitivity of mTORC1 in cells. A lower resolution structure of human Sestrin2 (PDB ID, 5CUF), which was crystallized in the absence of exogenous leucine, showed Sestrin2 to be in a nearly identical conformation as the leucine-bound structure. On the basis of this observation, it has been argued that leucine binding does not affect the conformation of Sestrin2 and that Sestrin2 may not be a sensor for leucine. We show that simple analysis of the reported "apo"-Sestrin2 structure reveals the clear presence of prominent, unmodeled electron density in the leucine-binding pocket that exactly accommodates the leucine observed in the higher resolution structure. Refining the reported apo-structure with leucine eliminated the large Fobs-Fcalc difference density at this position and improved the working and free R factors of the model. Consistent with this result, our own structure of Sestrin2 crystallized in the absence of exogenous leucine also contained electron density that is best explained by leucine. Thus, the structure of apo-Sestrin2 remains elusive.


    Related Citations: 
    • Structural basis for leucine sensing by the Sestrin2-mTORC1 pathway.
      Saxton, R.A.,Knockenhauer, K.E.,Wolfson, R.L.,Chantranupong, L.,Pacold, M.E.,Wang, T.,Schwartz, T.U.,Sabatini, D.M.
      (2016) Science 351: 53


    Organizational Affiliation

    Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, MA 02142, USA. Howard Hughes Medical Institute, Cambridge, MA 02139, USA. Koch Institute for Integrative Cancer Research, 77 Massachusetts Avenue, Cambridge, MA 02139, USA. Broad Institute of Harvard and Massachusetts Institute of Technology, 415 Main Street, Cambridge, MA 02142, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Sestrin-2
A, B, C, D, E
480Homo sapiensGene Names: SESN2 (SEST2)
Find proteins for P58004 (Homo sapiens)
Go to Gene View: SESN2
Go to UniProtKB:  P58004
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
LEU
Query on LEU

Download SDF File 
Download CCD File 
A, B, C, D, E
LEUCINE
C6 H13 N O2
ROHFNLRQFUQHCH-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.004 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.189 
  • Space Group: I 2 3
  • Diffraction Data DOI: 
    10.15785/SBGRID/528 SBGrid
Unit Cell:
Length (Å)Angle (°)
a = 292.263α = 90.00
b = 292.263β = 90.00
c = 292.263γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Cancer InstituteUnited StatesR01CA10386
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesAI47389
U.S. Department of DefenseUnited StatesW81XWH-07- 0448

Revision History 

  • Version 1.0: 2016-10-05
    Type: Initial release
  • Version 1.1: 2016-11-09
    Type: Structure summary
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence, Derived calculations