6N3E

Structure of HIV Tat-specific factor 1 U2AF Homology Motif bound to U2AF ligand motif 4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The pre-mRNA splicing and transcription factor Tat-SF1 is a functional partner of the spliceosome SF3b1 subunit via a U2AF homology motif interface.

Loerch, S.Leach, J.R.Horner, S.W.Maji, D.Jenkins, J.L.Pulvino, M.J.Kielkopf, C.L.

(2019) J Biol Chem 294: 2892-2902

  • DOI: https://doi.org/10.1074/jbc.RA118.006764
  • Primary Citation of Related Structures:  
    6N3D, 6N3E, 6N3F

  • PubMed Abstract: 

    The transcription elongation and pre-mRNA splicing factor Tat-SF1 associates with the U2 small nuclear ribonucleoprotein (snRNP) of the spliceosome. However, the direct binding partner and underlying interactions mediating the Tat-SF1-U2 snRNP association remain unknown. Here, we identified SF3b1 as a Tat-SF1-interacting subunit of the U2 snRNP. Our 1.1 Å resolution crystal structure revealed that Tat-SF1 contains a U2AF homology motif (UHM) protein-protein interaction module. We demonstrated that Tat-SF1 preferentially and directly binds the SF3b1 subunit compared with other U2AF ligand motif (ULM)-containing splicing factors, and further established that SF3b1 association depends on the integrity of the Tat-SF1 UHM. We next compared the Tat-SF1-binding affinities for each of the five known SF3b1 ULMs and then determined the structures of representative high- and low-affinity SF3b1 ULM complexes with the Tat-SF1 UHM at 1.9 Å and 2.1 Å resolutions, respectively. These structures revealed a canonical UHM-ULM interface, comprising a Tat-SF1 binding pocket for a ULM tryptophan (SF3b1 Trp 338 ) and electrostatic interactions with a basic ULM tail. Importantly, we found that SF3b1 regulates Tat-SF1 levels and that these two factors influence expression of overlapping representative transcripts, consistent with a functional partnership of Tat-SF1 and SF3b1. Altogether, these results define a new molecular interface of the Tat-SF1-U2 snRNP complex for gene regulation.


  • Organizational Affiliation

    From the Center for RNA Biology, Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HIV Tat-specific factor 196Homo sapiensMutation(s): 0 
Gene Names: HTATSF1
UniProt & NIH Common Fund Data Resources
Find proteins for O43719 (Homo sapiens)
Explore O43719 
Go to UniProtKB:  O43719
PHAROS:  O43719
GTEx:  ENSG00000102241 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43719
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SF3b1 U2AF ligand motif7Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for O75533 (Homo sapiens)
Explore O75533 
Go to UniProtKB:  O75533
PHAROS:  O75533
GTEx:  ENSG00000115524 
Entity Groups  
UniProt GroupO75533
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.198 
  • R-Value Work: 0.171 
  • R-Value Observed: 0.174 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.37α = 90
b = 58.37β = 90
c = 97.31γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM117005
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM070503

Revision History  (Full details and data files)

  • Version 1.0: 2019-01-02
    Type: Initial release
  • Version 1.1: 2019-03-06
    Changes: Data collection, Database references
  • Version 1.2: 2019-12-18
    Changes: Author supporting evidence
  • Version 1.3: 2024-03-13
    Changes: Data collection, Database references