4MI8

Crystal structure of the complex of murine gamma-herpesvirus 68 Bcl-2 homolog M11 and a Beclin 1 BH3 domain-derived peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Targeting gamma-herpesvirus 68 Bcl-2-mediated down-regulation of autophagy.

Su, M.Mei, Y.Sanishvili, R.Levine, B.Colbert, C.L.Sinha, S.

(2014) J Biol Chem 289: 8029-8040

  • DOI: 10.1074/jbc.M113.515361
  • Primary Citation of Related Structures:  
    4MI8

  • PubMed Abstract: 
  • γ-herpesviruses (γHVs) are common human pathogens that encode homologs of the anti-apoptotic cellular Bcl-2 proteins, which are critical to viral reactivation and oncogenic transformation. The murine γHV68 provides a tractable in vivo model for under ...

    γ-herpesviruses (γHVs) are common human pathogens that encode homologs of the anti-apoptotic cellular Bcl-2 proteins, which are critical to viral reactivation and oncogenic transformation. The murine γHV68 provides a tractable in vivo model for understanding general features of these important human pathogens. Bcl-XL, a cellular Bcl-2 homolog, and the murine γHV68 Bcl-2 homolog, M11, both bind to a BH3 domain within the key autophagy effector Beclin 1 with comparable affinities, resulting in the down-regulation of Beclin 1-mediated autophagy. Despite this similarity, differences in residues lining the binding site of M11 and Bcl-XL dictate varying affinities for the different BH3 domain-containing proteins. Here we delineate Beclin 1 differential specificity determinants for binding to M11 or Bcl-XL by quantifying autophagy levels in cells expressing different Beclin 1 mutants and either M11 or Bcl-XL, and we show that a G120E/D121A Beclin 1 mutant selectively prevents down-regulation of Beclin 1-mediated autophagy by Bcl-XL, but not by M11. We use isothermal titration calorimetry to identify a Beclin 1 BH3 domain-derived peptide that selectively binds to M11, but not to Bcl-XL. The x-ray crystal structure of this peptide bound to M11 reveals the mechanism by which the M11 BH3 domain-binding groove accommodates this M11-specific peptide. This information was used to develop a cell-permeable peptide inhibitor that selectively inhibits M11-mediated, but not Bcl-XL-mediated, down-regulation of autophagy.


    Organizational Affiliation

    From the Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Bcl-2 homolog (Gene 16?)AB143Murid gammaherpesvirus 4Mutation(s): 0 
Gene Names: GAMMAHV.M11M11v-bcl-2v-bcl-2 GAMMAHV.M11vBCL2
Find proteins for P89884 (Murid herpesvirus 4)
Explore P89884 
Go to UniProtKB:  P89884
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Beclin-1CD26Homo sapiensMutation(s): 2 
Gene Names: BECN1GT197
Find proteins for Q14457 (Homo sapiens)
Explore Q14457 
Go to UniProtKB:  Q14457
NIH Common Fund Data Resources
PHAROS  Q14457
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.156 
  • R-Value Observed: 0.160 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 70.598α = 90
b = 140.844β = 127.81
c = 54.038γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
MOLREPphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-01-29
    Type: Initial release
  • Version 1.1: 2014-10-08
    Changes: Database references
  • Version 1.2: 2016-02-17
    Changes: Structure summary