4L1U

Crystal Structure of Human Rtf1 Plus3 Domain in Complex with Spt5 CTR Phosphopeptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.424 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 

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.USA 110: 17290-17295

  • DOI: 10.1073/pnas.1314754110
  • Primary Citation of Related Structures:  

  • 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 rec ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase-associated protein RTF1 homolog
A, B, C, D, E, F
138Homo sapiensMutation(s): 0 
Gene Names: RTF1 (KIAA0252)
Find proteins for Q92541 (Homo sapiens)
Go to Gene View: RTF1
Go to UniProtKB:  Q92541
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Transcription elongation factor SPT5
G, H, I, J
13Homo sapiensMutation(s): 0 
Gene Names: SUPT5H (SPT5, SPT5H)
Find proteins for O00267 (Homo sapiens)
Go to Gene View: SUPT5H
Go to UniProtKB:  O00267
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B, C, D, E, F
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A, C, D, F
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
TPO
Query on TPO
G, H, I, J
L-PEPTIDE LINKINGC4 H10 N O6 PTHR
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.424 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 112.932α = 90.00
b = 172.514β = 107.00
c = 58.476γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
PHASERphasing
PDB_EXTRACTdata extraction
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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