4AC9

CRYSTAL STRUCTURE OF TRANSLATION ELONGATION FACTOR SELB FROM METHANOCOCCUS MARIPALUDIS IN COMPLEX WITH GDP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.03 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


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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:  
    4AC9, 4ACA, 4ACB

  • 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. 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 ...

    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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
MJ0495-LIKE PROTEINA, B, C, D482Methanococcus maripaludisMutation(s): 0 
Gene Names: selB, MMJJ_15030
UniProt
Find proteins for Q8J307 (Methanococcus maripaludis)
Explore Q8J307 
Go to UniProtKB:  Q8J307
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8J307
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GDP
Query on GDP
Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
M [auth C]		GUANOSINE-5'-DIPHOSPHATE
C10 H15 N5 O11 P2
QGWNDRXFNXRZMB-UUOKFMHZSA-N		 Ligand Interaction
DXC
Query on DXC
Download Ideal Coordinates CCD File 
K [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
K [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
W [auth C],
X [auth C]
(3ALPHA,5BETA,12ALPHA)-3,12-DIHYDROXYCHOLAN-24-OIC ACID
C24 H40 O4
KXGVEGMKQFWNSR-LLQZFEROSA-N		 Ligand Interaction
5GP
Query on 5GP
Download Ideal Coordinates CCD File 
L [auth B]GUANOSINE-5'-MONOPHOSPHATE
C10 H14 N5 O8 P
RQFCJASXJCIDSX-UUOKFMHZSA-N		 Ligand Interaction
SO4
Query on SO4
Download Ideal Coordinates CCD File 
I [auth B],
J [auth B],
O [auth C],
P [auth C],
Q [auth C],
I [auth B],
J [auth B],
O [auth C],
P [auth C],
Q [auth C],
R [auth C],
Y [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
N [auth C]		MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-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: 3.03 Å
  • R-Value Free: 0.222 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.191 
  • Space Group: P 31 1 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 146.92α = 90
b = 146.92β = 90
c = 297.48γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
CNSphasing

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-08-22
    Type: Initial release