4L1P

Crystal Structure of Human Rtf1 Plus3 domain


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Structural basis for Spt5-mediated recruitment of the Paf1 complex to chromatin.

Wier, A.D.Mayekar, M.K.Heroux, A.Arndt, K.M.Vandemark, A.P.

(2013) Proc Natl Acad Sci U S A 110: 17290-17295

  • DOI: 10.1073/pnas.1314754110
  • Primary Citation of Related Structures:  
    4L1P, 4L1U

  • PubMed Abstract: 
  • Polymerase associated factor 1 complex (Paf1C) broadly influences gene expression by regulating chromatin structure and the recruitment of RNA-processing factors during transcription elongation. The Plus3 domain of the Rtf1 subunit mediates Paf1C recruitment to genes by binding a repeating domain within the elongation factor Spt5 (suppressor of Ty) ...

    Polymerase associated factor 1 complex (Paf1C) broadly influences gene expression by regulating chromatin structure and the recruitment of RNA-processing factors during transcription elongation. The Plus3 domain of the Rtf1 subunit mediates Paf1C recruitment to genes by binding a repeating domain within the elongation factor Spt5 (suppressor of Ty). Here we provide a molecular description of this interaction by reporting the structure of human Rtf1 Plus3 in complex with a phosphorylated Spt5 repeat. We find that Spt5 binding is mediated by an extended surface containing phosphothreonine recognition and hydrophobic interfaces that interact with residues outside the Spt5 motif. Changes within these interfaces diminish binding of Spt5 in vitro and chromatin localization of Rtf1 in vivo. The structure reveals the basis for recognition of the repeat motif of Spt5, a key player in the recruitment of gene regulatory factors to RNA polymerase II.


    Organizational Affiliation

    Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA 15260.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homologB [auth A],
A [auth B]
138Homo sapiensMutation(s): 0 
Gene Names: KIAA0252RTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92541 (Homo sapiens)
Explore Q92541 
Go to UniProtKB:  Q92541
PHAROS:  Q92541
GTEx:  ENSG00000137815 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92541
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.12 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.206 
  • R-Value Observed: 0.208 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 33.636α = 90
b = 68.025β = 90
c = 116.972γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-10-02
    Type: Initial release
  • Version 1.1: 2013-10-23
    Changes: Database references
  • Version 1.2: 2013-11-20
    Changes: Database references
  • Version 1.3: 2017-11-15
    Changes: Refinement description