4L1U

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.42 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 

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: https://doi.org/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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
RNA polymerase-associated protein RTF1 homolog
A, B, C, D, E, F
A, B, C, D, E, F
138Homo sapiensMutation(s): 0 
Gene Names: KIAA0252, RTF1
UniProt & NIH Common Fund Data Resources
Find proteins for Q92541 (Homo sapiens)
Explore Q92541 
Go to UniProtKB:  Q92541
PHAROS:  Q92541
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92541
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Transcription elongation factor SPT5G, H, I, J13Homo sapiensMutation(s): 0 
Gene Names: SUPT5H, SPT5, SPT5H
UniProt & NIH Common Fund Data Resources
Find proteins for O00267 (Homo sapiens)
Explore O00267 
Go to UniProtKB:  O00267
PHAROS:  O00267
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00267
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4
Download Ideal Coordinates CCD File 
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
AA [auth D],
BA [auth D],
CA [auth D],
DA [auth D],
EA [auth D],
FA [auth D],
GA [auth D],
IA [auth E],
JA [auth E],
K [auth A],
KA [auth E],
L [auth A],
LA [auth E],
M [auth A],
MA [auth E],
NA [auth F],
O [auth B],
OA [auth F],
P [auth B],
PA [auth F],
Q [auth B],
R [auth B],
S [auth B],
T [auth B],
U [auth B],
V [auth C],
W [auth C],
X [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
Download Ideal Coordinates CCD File 
HA [auth D],
N [auth A],
QA [auth F],
Z [auth C]		GLYCEROL
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: 2.42 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.178 
  • R-Value Observed: 0.180 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 112.932α = 90
b = 172.514β = 107
c = 58.476γ = 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