8T5Q

SARS-CoV-2 ORF3a peptide in complex with TRAF2 TRAF domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

SARS-CoV-2 ORF3a-Mediated NF-kappa B Activation Is Not Dependent on TRAF-Binding Sequence.

Busscher, B.M.Befekadu, H.B.Liu, Z.Xiao, T.S.

(2023) Viruses 15

  • DOI: https://doi.org/10.3390/v15112229
  • Primary Citation of Related Structures:  
    8T5P, 8T5Q

  • PubMed Abstract: 

    Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has caused a global pandemic of Coronavirus Disease 2019 (COVID-19). Excessive inflammation is a hallmark of severe COVID-19, and several proteins encoded in the SARS-CoV-2 genome are capable of stimulating inflammatory pathways. Among these, the accessory protein open reading frame 3a (ORF3a) has been implicated in COVID-19 pathology. Here we investigated the roles of ORF3a in binding to TNF receptor-associated factor (TRAF) proteins and inducing nuclear factor kappa B (NF-κB) activation. X-ray crystallography and a fluorescence polarization assay revealed low-affinity binding between an ORF3a N-terminal peptide and TRAFs, and a dual-luciferase assay demonstrated NF-κB activation by ORF3a. Nonetheless, mutation of the N-terminal TRAF-binding sequence PIQAS in ORF3a did not significantly diminish NF-κB activation in our assay. Our results thus suggest that the SARS-CoV-2 protein may activate NF-κB through alternative mechanisms.


  • Organizational Affiliation

    Department of Pathology, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TNF receptor-associated factor 2
A, B, C, D, E
A, B, C, D, E, F
188Homo sapiensMutation(s): 0 
Gene Names: TRAF2TRAP3
EC: 2.3.2.27
UniProt & NIH Common Fund Data Resources
Find proteins for Q12933 (Homo sapiens)
Explore Q12933 
Go to UniProtKB:  Q12933
PHAROS:  Q12933
GTEx:  ENSG00000127191 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ12933
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
ORF3a protein
G, H, I
5Severe acute respiratory syndrome coronavirus 2Mutation(s): 0 
UniProt
Find proteins for P0DTC3 (Severe acute respiratory syndrome coronavirus 2)
Explore P0DTC3 
Go to UniProtKB:  P0DTC3
Entity Groups  
UniProt GroupP0DTC3
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PG4
Query on PG4

Download Ideal Coordinates CCD File 
J [auth A],
K [auth B],
N [auth D],
Q [auth F]
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
L [auth C],
M [auth C],
O [auth E],
P [auth E]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.2α = 90
b = 84.22β = 118.82
c = 124.39γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesAI141350
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM127609

Revision History  (Full details and data files)

  • Version 1.0: 2023-11-29
    Type: Initial release
  • Version 1.1: 2023-12-06
    Changes: Database references