6JI2

Crystal structure of archaeal ribosomal protein aP1, aPelota, and GTP-bound aEF1A complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Switch of the interactions between the ribosomal stalk and EF1A in the GTP- and GDP-bound conformations.

Maruyama, K.Imai, H.Kawamura, M.Ishino, S.Ishino, Y.Ito, K.Uchiumi, T.

(2019) Sci Rep 9: 14761-14761

  • DOI: 10.1038/s41598-019-51266-x
  • Primary Citation of Related Structures:  
    6JI2

  • PubMed Abstract: 
  • Translation elongation factor EF1A delivers aminoacyl-tRNA to the ribosome in a GTP-bound form, and is released from the ribosome in a GDP-bound form. This association/dissociation cycle proceeds efficiently via a marked conformational change in EF1A. EF1A function is dependent on the ribosomal "stalk" protein of the ribosomal large subunit, although the precise mechanism of action of the stalk on EF1A remains unclear ...

    Translation elongation factor EF1A delivers aminoacyl-tRNA to the ribosome in a GTP-bound form, and is released from the ribosome in a GDP-bound form. This association/dissociation cycle proceeds efficiently via a marked conformational change in EF1A. EF1A function is dependent on the ribosomal "stalk" protein of the ribosomal large subunit, although the precise mechanism of action of the stalk on EF1A remains unclear. Here, we clarify the binding mode of archaeal stalk aP1 to GTP-bound aEF1A associated with aPelota. Intriguingly, the C-terminal domain (CTD) of aP1 binds to aEF1A•GTP with a similar affinity to aEF1A•GDP. We have also determined the crystal structure of the aP1-CTD•aEF1A•GTP•aPelota complex at 3.0 Å resolution. The structure shows that aP1-CTD binds to a space between domains 1 and 3 of aEF1A. Biochemical analyses show that this binding is crucial for protein synthesis. Comparison of the structures of aP1-CTD•aEF1A•GTP and aP1-CTD•aEF1A•GDP demonstrates that the binding mode of aP1 changes markedly upon a conformational switch between the GTP- and GDP-bound forms of aEF1A. Taking into account biochemical data, we infer that aP1 employs its structural flexibility to bind to aEF1A before and after GTP hydrolysis for efficient protein synthesis.


    Organizational Affiliation

    Department of Biology, Faculty of Science, Niigata University, Ikarashi 2-8050, Niigata, 950-2181, Japan. uchiumi@bio.sc.niigata-u.ac.jp.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Elongation factor 1-alpha AE447Aeropyrum pernix K1Mutation(s): 0 
Gene Names: tufAPE_1844
Find proteins for Q9YAV0 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YAV0 
Go to UniProtKB:  Q9YAV0
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein pelota homolog BF376Aeropyrum pernix K1Mutation(s): 0 
Gene Names: pelAAPE_1800.1
EC: 3.1
Find proteins for Q9YAZ5 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9YAZ5 
Go to UniProtKB:  Q9YAZ5
Protein Feature View
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  • Reference Sequence
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Archaeal ribosomal stalk protein aP1 X17Aeropyrum pernix K1Mutation(s): 0 
Gene Names: rpl12APE_2170
Find proteins for Q9Y9W9 (Aeropyrum pernix (strain ATCC 700893 / DSM 11879 / JCM 9820 / NBRC 100138 / K1))
Explore Q9Y9W9 
Go to UniProtKB:  Q9Y9W9
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTP
Query on GTP

Download Ideal Coordinates CCD File 
A, E
GUANOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O14 P3
XKMLYUALXHKNFT-UUOKFMHZSA-N
 Ligand Interaction
MG
Query on MG

Download Ideal Coordinates CCD File 
A, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download Ideal Coordinates CCD File 
A, E
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.203 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.447α = 98.64
b = 73.405β = 93.8
c = 108.142γ = 100.44
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
BALBESphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2019-11-13
    Type: Initial release