4D4P

Crystal Structure of the Kti11 Kti13 heterodimer Spacegroup P65


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 

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:  
    4D4O, 4D4P, 4D4Q

  • 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-dependent tRNA wobble base modifications, thereby affecting the speed and accuracy of protein biosynthesis through two distinct mechanisms ...

    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. Electronic address: cmueller@embl.de.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PROTEIN ATS1, DIPHTHAMIDE BIOSYNTHESIS PROTEIN 3A, B, C, D [auth E], E [auth G], F [auth H]427Saccharomyces cerevisiaeMutation(s): 0 
UniProt
Find proteins for Q3E840 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore Q3E840 
Go to UniProtKB:  Q3E840
Find proteins for P31386 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P31386 
Go to UniProtKB:  P31386
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.209 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 152.06α = 90
b = 152.06β = 90
c = 203.85γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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