4ACA

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS, APO FORM


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Selenocysteine tRNA-Specific Elongation Factor Selb is a Structural Chimaera of Elongation and Initiation Factors.

Leibundgut, M.Frick, C.Thanbichler, M.Bock, A.Ban, N.

(2005) Embo J. 24: 11

  • DOI: 10.1038/sj.emboj.7600505
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. He ...

    In all three kingdoms of life, SelB is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a UGA stop codon in the presence of a downstream mRNA hairpin loop. Here, we present the X-ray structures of SelB from the archaeon Methanococcus maripaludis in the apo-, GDP- and GppNHp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. All three SelB structures reveal an EF-Tu:GTP-like domain arrangement. Upon binding of the GTP analogue GppNHp, a conformational change of the Switch 2 region in the GTPase domain leads to the exposure of SelB residues involved in clamping the 5' phosphate of the tRNA. A conserved extended loop in domain III of SelB may be responsible for specific interactions with tRNA(Sec) and act as a ruler for measuring the extra long acceptor arm. Domain IV of SelB adopts a beta barrel fold and is flexibly tethered to domain III. The overall domain arrangement of SelB resembles a 'chalice' observed so far only for initiation factor IF2/eIF5B. In our model of SelB bound to the ribosome, domain IV points towards the 3' mRNA entrance cleft ready to interact with the downstream secondary structure element.


    Organizational Affiliation

    Institut für Molekularbiologie und Biophysik, Eidgenössische Technische Hochschule Zürich, Zürich, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TRANSLATION ELONGATION FACTOR SELB
A, B, C, D
482Methanococcus maripaludisMutation(s): 0 
Gene Names: selB
Find proteins for Q8J307 (Methanococcus maripaludis)
Go to UniProtKB:  Q8J307
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
5GP
Query on 5GP

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Download CCD File 
B
GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N
 Ligand Interaction
DXC
Query on DXC

Download SDF File 
Download CCD File 
B, C
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
DEOXYCHOLIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CMH
Query on CMH
A, B, C, D
L-PEPTIDE LINKINGC4 H9 Hg N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.15 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.172 
  • Space Group: P 31 1 2
Unit Cell:
Length (Å)Angle (°)
a = 146.860α = 90.00
b = 146.860β = 90.00
c = 297.830γ = 120.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release