8YTF

Crystal structures of human IRF2BP2 RING domain in complex with VGLL4 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 

Starting Model: in silico
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wwPDB Validation   3D Report Full Report


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Literature

IRF2BP2 binds to a conserved RxSVI motif of protein partners and regulates megakaryocytic differentiation.

Wang, G.Lu, T.Zhang, L.Ding, J.

(2024) Nat Commun 15: 10425-10425

  • DOI: https://doi.org/10.1038/s41467-024-54889-5
  • Primary Citation of Related Structures:  
    8YTF, 8YTG, 8YTH

  • PubMed Abstract: 

    IRF2BP2 is a transcriptional coregulator that plays diverse regulatory roles in various cellular processes in either IRF2-dependent or IRF2-independent manner through interactions with protein partners via its RING domain; however, the underlying molecular mechanisms remain unclear. In this study, we conduct a motif discovery search on the sequences of interacting proteins IRF2 and VGLL4 of IRF2BP2 and identify a conserved RxSVI motif. Biochemical and structural data reveal that the RING domain binds to the motif-containing peptides of IRF2 and VGLL4 with comparable affinities and in a similar manner. The motif-containing peptides tend to form a short loop along with a short β-strand, which facilitates effective recognition and tight binding by the RING domain. Further exploration of this motif in the human proteome identifies the transcription factor ZBTB16 as an interacting protein of IRF2BP2. Biochemical, structural, and cell biological data demonstrate that the RING domain binds to the motif-containing peptide of ZBTB16 in a manner similar to that of IRF2 and VGLL4. Moreover, IRF2BP2 plays a crucial regulatory role in megakaryocytic differentiation through interaction with ZBTB16. These findings elucidate the molecular basis for how IRF2BP2 can engage with different protein partners, thereby exerting diverse regulatory functions in many cellular processes.


  • Organizational Affiliation

    Key Laboratory of RNA Innovation, Science and Engineering, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Interferon regulatory factor 2-binding protein 283Homo sapiensMutation(s): 0 
Gene Names: IRF2BP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z5L9 (Homo sapiens)
Explore Q7Z5L9 
Go to UniProtKB:  Q7Z5L9
PHAROS:  Q7Z5L9
GTEx:  ENSG00000168264 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7Z5L9
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transcription cofactor vestigial-like protein 48Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for Q14135 (Homo sapiens)
Explore Q14135 
Go to UniProtKB:  Q14135
PHAROS:  Q14135
GTEx:  ENSG00000144560 
Entity Groups  
UniProt GroupQ14135
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.59 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.153 
  • R-Value Observed: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.372α = 90
b = 43.209β = 90
c = 55.761γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaXDB37030305

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-20
    Type: Initial release
  • Version 1.1: 2024-12-18
    Changes: Database references