4D4P

Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P65


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.999 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the Kti11/Kti13 Heterodimer and its Double Role in Modifications of tRNA and Eukaryotic Elongation Factor 2.

Glatt, S.Zabel, R.Vonkova, I.Kumar, A.Netz, D.J.Pierik, A.J.Rybin, V.Lill, R.Gavin, A.Balbach, J.Breunig, K.D.Muller, C.W.

(2015) Structure 23: 7

  • DOI: 10.1016/j.str.2014.11.008
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The small, highly conserved Kti11 alias Dph3 protein encoded by the Kluyveromyces lactis killer toxin insensitive gene KTI11/DPH3 is involved in the diphthamide modification of eukaryotic elongation factor 2 and, together with Kti13, in Elongator-dep ...

    The small, highly conserved Kti11 alias Dph3 protein encoded by the Kluyveromyces lactis killer toxin insensitive gene KTI11/DPH3 is involved in the diphthamide modification of eukaryotic elongation factor 2 and, together with Kti13, in Elongator-dependent tRNA wobble base modifications, thereby affecting the speed and accuracy of protein biosynthesis through two distinct mechanisms. We have solved the crystal structures of Saccharomyces cerevisiae Kti13 and the Kti11/Kti13 heterodimer at 2.4 and 2.9 Å resolution, respectively, and validated interacting residues through mutational analysis in vitro and in vivo. We show that metal coordination by Kti11 and its heterodimerization with Kti13 are essential for both translational control mechanisms. Our structural and functional analyses identify Kti13 as an additional component of the diphthamide modification pathway and provide insight into the molecular mechanisms that allow the Kti11/Kti13 heterodimer to coregulate two consecutive steps in ribosomal protein synthesis.


    Organizational Affiliation

    Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstraße 1, 69117 Heidelberg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3
A, B, C, E, G, H
427Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: ATS1, KTI11 (DPH3)
Find proteins for P31386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P31386
Find proteins for Q3E840 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  Q3E840
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

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

Download SDF File 
Download CCD File 
A, C, G, H
FE (III) ION
Fe
VTLYFUHAOXGGBS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.999 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • Space Group: P 65
Unit Cell:
Length (Å)Angle (°)
a = 152.060α = 90.00
b = 152.060β = 90.00
c = 203.850γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-01-14
    Type: Initial release
  • Version 1.1: 2017-03-15
    Type: Source and taxonomy
  • Version 1.2: 2017-08-23
    Type: Data collection