3CL3

Crystal Structure of a vFLIP-IKKgamma complex: Insights into viral activation of the IKK signalosome


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Crystal structure of a vFlip-IKKgamma complex: insights into viral activation of the IKK signalosome.

Bagneris, C.Ageichik, A.V.Cronin, N.Wallace, B.Collins, M.Boshoff, C.Waksman, G.Barrett, T.

(2008) Mol Cell 30: 620-631

  • DOI: https://doi.org/10.1016/j.molcel.2008.04.029
  • Primary Citation of Related Structures:  
    3CL3

  • PubMed Abstract: 

    Key to the pathogenicity of several viruses is activation of the canonical nuclear factor-kappaB (NF-kappaB) transcriptional pathway. Subversion of this tightly regulated mechanism is achieved through the production of host mimetic viral proteins that deregulate the transcription process. One such protein is ks-vFLIP (produced by the Kaposi's sarcoma herpes virus [KSHV]), which associates with IKKgamma, an essential component of the IKK complex or signalosome. This interaction renders the canonical NF-kappaB pathway constitutively active and has been linked to Kaposi's sarcoma and other malignancies. In order to elucidate the molecular basis underpinning ks-vFLIP-induced activation of the IKK signalosome, we have determined the crystal structure of a complex involving a fragment of IKKgamma bound to ks-vFLIP at 3.2 A. In addition to identifying and subsequently probing the ks-vFLIP-IKKgamma interface, we have also investigated the effects of a mutation implicated in the genetic disorder anhydrotic ectodermal dysplasia with immunodeficiency (EDA-ID).


  • Organizational Affiliation

    Institute of Structural and Molecular Biology, School of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ORF K13
A, B
183Human gammaherpesvirus 8Mutation(s): 0 
Gene Names: vFLIP
UniProt
Find proteins for Q76RF1 (Human herpesvirus 8)
Explore Q76RF1 
Go to UniProtKB:  Q76RF1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ76RF1
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
NF-kappa-B essential modulatorC [auth D],
D [auth E]
130Homo sapiensMutation(s): 0 
Gene Names: IKBKGFIP3NEMO
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y6K9 (Homo sapiens)
Explore Q9Y6K9 
Go to UniProtKB:  Q9Y6K9
PHAROS:  Q9Y6K9
GTEx:  ENSG00000269335 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y6K9
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.287 
  • R-Value Work: 0.261 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 145.67α = 90
b = 145.67β = 90
c = 101.54γ = 120
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2008-06-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2018-06-13
    Changes: Data collection, Database references, Source and taxonomy
  • Version 1.3: 2024-02-21
    Changes: Data collection, Database references