8SM5

Crystal Structure of BHRF1 from Epstein Barr Virus in complex with BID BH3 peptide

  • Classification: VIRAL PROTEIN
  • Organism(s): Human herpesvirus 4 strain B95-8, Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2023-04-25 Released: 2023-10-11 
  • Deposition Author(s): Wyatt, S., Sinha, S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Center for Research Resources (NIH/NCRR), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Science Foundation (NSF, United States)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Epstein-Barr Virus Encoded BCL2, BHRF1, Downregulates Autophagy by Noncanonical Binding of BECN1.

Wyatt, S.Glover, K.Dasanna, S.Lewison, M.Gonzalez-Garcia, M.Colbert, C.L.Sinha, S.C.

(2023) Biochemistry 62: 2934-2951

  • DOI: https://doi.org/10.1021/acs.biochem.3c00225
  • Primary Citation of Related Structures:  
    8SM5

  • PubMed Abstract: 

    γ-herpesviruses (γHVs) encode BCL2 homologues (vBCL2) that bind the Bcl-2 homology 3 domains (BH3Ds) of diverse proteins, inhibiting apoptosis and promoting host cell and virus survival. vBCLs encoded by Kaposi sarcoma-associated HV (KSHV) and γHV68 downregulate autophagy, a degradative cellular process crucial for homeostasis and innate immune responses to pathogens, by binding to a BH3D in BECN1, a key autophagy protein. Epstein-Barr virus (EBV) encodes a vBCL2 called BHRF1. Here we show that unlike the KSHV and γHV68 vBCL2s, BHRF1 does not bind the isolated BECN1 BH3D. We use yeast two-hybrid assays to identify the minimal region of BECN1 required and sufficient for binding BHRF1. We confirm that this is a direct, albeit weak, interaction via affinity pull-down assays and isothermal titration calorimetry. To understand the structural bases of BHRF1 specificity, we determined the 2.6 Å crystal structure of BHRF1 bound to the BID BH3D, which binds ∼400-times tighter to BHRF1 than does BECN1, and performed a detailed structural comparison with complexes of diverse BH3Ds bound to BHRF1 and to other antiapoptotic BCL2s. Lastly, we used mammalian cell autophagy assays to demonstrate that BHRF1 downregulates autophagy and that a cell-permeable peptide derived from the BID BH3D inhibits BHRF1-mediated downregulation of autophagy. In summary, our results suggest that BHRF1 downregulates autophagy by noncanonical binding of a flexible region of BECN1 that includes but is not limited to the BH3D and that BH3D-derived peptides that bind better to BHRF1 can block downregulation of autophagy by BHRF1.


  • Organizational Affiliation

    Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108-6050, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Apoptosis regulator BHRF1
A, C, E, G, I
156Human herpesvirus 4 strain B95-8Mutation(s): 0 
Gene Names: BHRF1
UniProt
Find proteins for P03182 (Epstein-Barr virus (strain B95-8))
Explore P03182 
Go to UniProtKB:  P03182
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP03182
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
BID BH3
B, D, F, H, J
18Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P55957 (Homo sapiens)
Explore P55957 
Go to UniProtKB:  P55957
PHAROS:  P55957
GTEx:  ENSG00000015475 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55957
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.61 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.198 
  • R-Value Observed: 0.201 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.817α = 90
b = 186.817β = 90
c = 70.486γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United States1R15GM146232
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesRO3NS090939
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR15 GM122035
National Institutes of Health/National Center for Research Resources (NIH/NCRR)United StatesP20 RR015566
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesR21 AI078198
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM126207
National Science Foundation (NSF, United States)United StatesMCB-1413525

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Database references
  • Version 1.2: 2024-03-06
    Changes: Database references, Source and taxonomy, Structure summary