6HIP

Structure of SPF45 UHM bound to HIV-1 Rev ULM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 

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This is version 1.2 of the entry. See complete history


Literature

Modulation of HIV-1 gene expression by binding of a ULM motif in the Rev protein to UHM-containing splicing factors.

Pabis, M.Corsini, L.Vincendeau, M.Tripsianes, K.Gibson, T.J.Brack-Werner, R.Sattler, M.

(2019) Nucleic Acids Res 47: 4859-4871

  • DOI: https://doi.org/10.1093/nar/gkz185
  • Primary Citation of Related Structures:  
    6HIP

  • PubMed Abstract: 

    The HIV-1 protein Rev is essential for virus replication and ensures the expression of partially spliced and unspliced transcripts. We identified a ULM (UHM ligand motif) motif in the Arginine-Rich Motif (ARM) of the Rev protein. ULMs (UHM ligand motif) mediate protein interactions during spliceosome assembly by binding to UHM (U2AF homology motifs) domains. Using NMR, biophysical methods and crystallography we show that the Rev ULM binds to the UHMs of U2AF65 and SPF45. The highly conserved Trp45 in the Rev ULM is crucial for UHM binding in vitro, for Rev co-precipitation with U2AF65 in human cells and for proper processing of HIV transcripts. Thus, Rev-ULM interactions with UHM splicing factors contribute to the regulation of HIV-1 transcript processing, also at the splicing level. The Rev ULM is an example of viral mimicry of host short linear motifs that enables the virus to interfere with the host molecular machinery.


  • Organizational Affiliation

    Institute of Structural Biology, Helmholtz Zentrum München, Neuherberg 85 764, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Splicing factor 45
A, B
104Homo sapiensMutation(s): 0 
Gene Names: RBM17SPF45
UniProt & NIH Common Fund Data Resources
Find proteins for Q96I25 (Homo sapiens)
Explore Q96I25 
Go to UniProtKB:  Q96I25
PHAROS:  Q96I25
GTEx:  ENSG00000134453 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96I25
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
HIV-1 Rev (41-49)9Human immunodeficiency virus 1Mutation(s): 0 
UniProt
Find proteins for P04618 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2))
Explore P04618 
Go to UniProtKB:  P04618
Entity Groups  
UniProt GroupP04618
Sequence Annotations
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.20 Å
  • R-Value Free: 0.175 
  • R-Value Work: 0.149 
  • R-Value Observed: 0.150 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 48.21α = 90
b = 63.68β = 90
c = 67.63γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Research FoundationGermanySFB1035

Revision History  (Full details and data files)

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-10-09
    Changes: Data collection, Database references
  • Version 1.2: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description