4TMV

Translation initiation factor eIF5B (517-858) from C. thermophilum, bound to GTPgammaS and Sodium


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

A monovalent cation acts as structural and catalytic cofactor in translational GTPases.

Kuhle, B.Ficner, R.

(2014) EMBO J 33: 2547-2563

  • DOI: https://doi.org/10.15252/embj.201488517
  • Primary Citation of Related Structures:  
    4TMT, 4TMV, 4TMW, 4TMX, 4TMZ, 4TN1

  • PubMed Abstract: 

    Translational GTPases are universally conserved GTP hydrolyzing enzymes, critical for fidelity and speed of ribosomal protein biosynthesis. Despite their central roles, the mechanisms of GTP-dependent conformational switching and GTP hydrolysis that govern the function of trGTPases remain poorly understood. Here, we provide biochemical and high-resolution structural evidence that eIF5B and aEF1A/EF-Tu bound to GTP or GTPγS coordinate a monovalent cation (M(+)) in their active site. Our data reveal that M(+) ions form constitutive components of the catalytic machinery in trGTPases acting as structural cofactor to stabilize the GTP-bound "on" state. Additionally, the M(+) ion provides a positive charge into the active site analogous to the arginine-finger in the Ras-RasGAP system indicating a similar role as catalytic element that stabilizes the transition state of the hydrolysis reaction. In sequence and structure, the coordination shell for the M(+) ion is, with exception of eIF2γ, highly conserved among trGTPases from bacteria to human. We therefore propose a universal mechanism of M(+)-dependent conformational switching and GTP hydrolysis among trGTPases with important consequences for the interpretation of available biochemical and structural data.


  • Organizational Affiliation

    Abteilung für Molekulare Strukturbiologie, Institut für Mikrobiologie und Genetik Göttinger Zentrum für Molekulare Biowissenschaften Georg-August-Universität Göttingen, Göttingen, Germany bkuhle@gwdg.de.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
eIF5BA [auth B],
B [auth A]
345Thermochaetoides thermophilaMutation(s): 0 
EC: 3.6.5.3
UniProt
Find proteins for G0S8G9 (Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719))
Explore G0S8G9 
Go to UniProtKB:  G0S8G9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupG0S8G9
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GSP
Query on GSP

Download Ideal Coordinates CCD File 
C [auth B],
J [auth A]
5'-GUANOSINE-DIPHOSPHATE-MONOTHIOPHOSPHATE
C10 H16 N5 O13 P3 S
XOFLBQFBSOEHOG-UUOKFMHZSA-N
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth B]
G [auth B]
H [auth B]
I [auth B]
M [auth A]
F [auth B],
G [auth B],
H [auth B],
I [auth B],
M [auth A],
N [auth A],
O [auth A]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
MG
Query on MG

Download Ideal Coordinates CCD File 
D [auth B],
K [auth A]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
E [auth B],
L [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.53 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 55.64α = 90
b = 115.85β = 101.35
c = 66.09γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
X-PLORmodel building
PDB_EXTRACTdata extraction
PHASERphasing
PHENIXrefinement
XSCALEdata reduction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-09-24
    Type: Initial release
  • Version 1.1: 2014-11-19
    Changes: Database references
  • Version 1.2: 2016-02-24
    Changes: Structure summary
  • Version 1.3: 2018-03-07
    Changes: Data collection, Source and taxonomy
  • Version 1.4: 2023-12-20
    Changes: Data collection, Database references, Derived calculations, Refinement description